You need to create an external manifest file, and ensure that PowerBuilder does not try to generate an internal one in the executable. Forturnately, I don't believe PB 5 could do that. It only started becoming an option when PB introduced support for new style controls.
As long as the manifest file has the same name as the PowerBuilder generated executable with a ".manifest" extension, Windows will use it. It's not a question of whether or not PowerBuilder will work with it, but whether Windows will. Of course, you have to be a on fairly recent version of Windows. If you're still using PowerBuilder 5, you might still be using Windows 95. What version of Windows are you using?
Manifest files are pretty tricky to put together by hand. I suggest looking at something like Side by Side Manifest Maker that will generate them for you.