Can we integrate Citrix 5.0 and 6.5 in the same APM portal?

For option 1, check on your VS is the box VDI, PerAPP VPN is checked. This enable ICA proxy on the VS.

For option 2, your admin has to allow XML request on the Broker. If you look in the deployment guide, there is a section for that (Appendix)

In both cases, the VDI box has to be checked on the Virtual Server

I would advice to re-run the iApp with SF replacement so that you can check what the iApps does. It's not really difficult but you have to understand how APM works with ICA.