You can certainly do that and it's a better practice than making one big MSI.  You also have a good idea to make a wrapper and not nest MSIs - that can drive folks nuts.

Can i capture each exe (except the dongle exe) , do all the customization (Like Uncheck desktop shortcut, CA guidlines) create an msi for each exe and then create a wrapper.exe to run all the msi's .
I have never tried this but will want try it, please give me some reviews  on it

Thanks Arminius , i am very sure that the suite (InteliGen NT) doesnot extract any msi file.

1 - As per your comment, i found a switch ( /silent) to each exe , but again the problem is the client doesnt want a desktop shortcut (each exe has a check box to add desktop shortcut when installed in UI mode) , but this is not a big issue, can do some tweaks to remove it.

2  - I have capture the entire setup , and found that the 10 out 12 exe's can be added to a script , and the dongle one will have to be install with the some other method , searching on google if there is any possible way to get through this,

please let me know any more view or advise on it

Thanks,

Another way to find out if an MSI is extracted (and where) is to start a setup capture by pointing at notepad.exe. Once the capture starts and notepad appears, minimize it (don't close it) and then start your setup.exe. Once it has started and extracted its files, leave the setup.exe open, close notepad.exe and then complete the capture. The result should give you a list of all the files extracted by the original setup.exe. Repeat as required to drill down into the other extracted exe's.

FYI, this is a great trick if you have an app that does configuration post install and you want to know what changes were made.

When I've seen messes like this, it becomes a challenge to determine exactly what is going to be installed.  If you don't have an app owner, get one or it will be you and you'll never have this off your plate.

The only way to be really sure that an MSI isn't extracted somewhere is to run the install and watch for msiexec to start.  If it starts, you've got an MSI somewhere. 

There are really 2 ways of doing this:

1.  Extract the files, figure out how to install each exe silently, then script your install to call each exe silently in order, suppressing reboots until the end.  Depending on how the setup exe files were written, this may work or it may not.  Older apps or poorly designed apps are going to reboot, no matter what you do. 
2.  Snapshot the entire mess, make one MSI, and figure out how to make vendor updates work. 

Dongle drivers can be interesting - I've seen apps where the install won't happen without the dongle.  You'll want to ensure that it will install without the dongle; otherwise you'll need a dongle to package this. 

There's a lot more detail I could go into; hope this is a good starting point.