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How to add add some msi application to visual studio InstallShield Redistributables?

I used Visual Studio 2015 InstallShield Limited Edition Project to create my application setup.
My application must be installed api.msi, .net3.5 and .net4.5 to be exeuted.
In "Specify Application Data->Redistributables", I only can add .net3.5 and .net 4.5 to my setup. but i can't add api.msi to Redistributables.
How do i add api.msi to Redistributables?
this is my Redistributables
I hope the installation steps are as follows
run setup->set install path->install .net(3.5 and 4.5) & api.msi & application.

Best way to do it is by creating merge module and add it to your project for details refer the link

InstallShield can include either merge modules or prerequisites, but the Limited and Express editions do not include the capabilities to build either. Both options are available with the Professional and higher editions, and other tools may be able to create merge modules.

You can download an eval copy of InstallShield and throw it on a VM. Build your setup prereq file (.PRQ) for it. Copy the PRQ and api.msi to your machine with InstallShield LE and consume it.
You can read more about how to author a PRQ here: (Disclosure: My blog article from 11 years ago)
http://iswix.com/2006/11/21/using-installshield-12-to-install-net-framework-3-0/
I maintain an open source project called IsWiX that creates graphical UIs for managing XML documents. I thought about creating a tool to maintain PRQ files. It would only take me a day to write it but I was concerned Flexera might get really irritated. :)

Alternatives to using MSI's - MSBuild?

I work in an environment that has leaned heavy on the use of MSI's. With the latest versions of Visual Studio this type of deployment setup is no longer provided. I've heard that using MSBuild is the preferred alternative. Does MSBuild create a file / other that a team could run on production servers? Developers do not have permissions to prod servers here. We have to pass our msi's to another team to run them.
Any help would be appreciated.

Visual Studio Deployment Projects (aka VDPROJ) deprecated from Visual Studio 2012. The output of VDPROJ is MSI.
Microsoft recommendation is WIX as a replacement for creating MSI installers. WIX is an XML based (.wixproj) project.
Don't confuse MSBuild with WIX. MSBuild is a build engine for generating code from XML based projects (.csproj, vbproj, etc.).

You can use Wix
There is a steep learning curve, but it is very powerful

Use WiX toolset - it is a nice alternative and integrates well with visual studio and team build.
http://wixtoolset.org/

Visual Studio version-agnostic projects/solutions: is it possible?

I remember seeing an open source project within the last year that I was able to open in both VS 2008 and VS 2010 without an upgrade wizard popping up. I think...
Is it possible to create a project/solution that will open up in any version of Visual Studio without prompting me to run the upgrade wizard? If so, how do I do this?
Information for both C++ and C# projects would be most helpful.

You can, use CMake and generate VSx solution.
I think the project that you have seen had 2 visual studio solutions for different visual studio versions.
Update:
Also, you can use http://sourceforge.net/projects/vspc/
or see http://www.emmet-gray.com/Articles/ProjectConverter.htm

The solution format hasn't changed significantly over the visual studio versions except the version number.
If the code itself is generic enough (not using linq, etc) then you can edit the first line of the solution file to "downgrade" the version.
VS2005 uses:
Microsoft Visual Studio Solution File, Format Version 9.00
# Visual Studio 2005

You can give the Prebuild project a try to generate needed solution files on the fly.
Prebuild is a cross-platform XML-driven pre-build tool which allows
developers to easily generate project files for major IDE's and .NET
development tools including: Visual Studio .NET 2002, 2003, 2005, 2008, 2010
SharpDevelop, MonoDevelop, NAnt and Autotools.

May be it is not what you ask about, but you can convert you project into nmake target

The only way to do this is to create separate solutions (for 2010 and 2008), and include existing projects to different solutions. Create new projects in VS2008, and then add them to VS2010 solution.

You may need something like round-tripping
Round-tripping is the ability to use a current or previous version of Visual Studio to target a platform that is supported by both versions of VS. For example, with round-tripping, you can open projects from a previous version of VS in a newer IDE without the need for conversion, thus allowing you to work side-by-side on old and upgraded projects.
Read more

how to create setup files in c#

i like to setup for my project i did my project in Microsoft visual studio c#.net 2008, where i have start for that

I'm surprised noone has mentioned this yet:
Windows Installer XML (WiX) toolset
Open source, from Microsoft. (Yes, you read that right).
Free to use, yet very capable (used to create the Microsoft Office 2007 installer).
Based on commandline tools, so easily integrated into a build system.
My speculation: Since Rob Mensching (the primary author) has just moved into the Visual Studio team at Microsoft, this is likely to be directly supported (in some form) in the version of Visual Studio following 2010.
Update: An interesting interview with Rob Mensching on Hanselminutes. On the show, Rob talks about how WiX is more than 10 years old, though the first public release was April 5, 2004.

Are you looking for an installer you can use the following free tools, if you want to pay, install shield is good:
Built into VS:
http://msdn.microsoft.com/en-us/library/ms173084(VS.80).aspx
http://msdn.microsoft.com/en-us/library/2kt85ked(VS.80).aspx
Other free tools:
http://nsis.sourceforge.net/Main_Page
http://www.installjammer.com/
Install shield:
http://www.flexerasoftware.com/products/installshield.htm
Wise:
http://www.wise.com/Products/Installations/WiseInstallerEvaluations.aspx

You will have to add a new Setup and Deployment project to your solution. Here is a nice step by step instructions.
Note: Which version of VS are you using? I am not sure whether this project type is available in Express Edition.

I use Inno Setup with ISTool (both are free) to create setup for my .NET C# applications.
Play around with ISTool and simply include your application files into the setup. Then configure to Download and install .NET redistributable and other components when required.

How to generate Make File in Visual Studio 2008 Express Edition

Does anybody know how to generate Make File in Visual Studio C# 2008 Express Edition?

Make files have little to no use in .NET world. Rather, consider using MSBuild.

Try this:
Download MonoDevelop 2.0
Open solution.
Right click on solution name -> Generate makefiles...

Makefiles are really used for cross platform compiling or working with other build systems. When you are working with C# you are only really going to be compiling with Microsoft's tools or using Mono on another platform, so I don't think that you can. An alternative could be NAnt however depending on what you want to use your Makefile for.