How c an I download my old apps on my new Iphone?

If the process of transferring data from old iPhone to new iPhone skips some apps.. it's likely because those apps are no longer supported on newer iOS versions.

You don't upload apps.. you download them.. from the App Store. Even when transferring from old phone to new, it's really going out to the App Store and downloading a new copy.

You should be able to download them from the Apple App Store. Have you tried doing so yet? Note that some apps may no longer be available as they may be incompatible with the newer version of iOS running on your new iPhone SE.