1) should I keep both P3D4 & 5 checked while running installer?
Normally yes but, if it's already installed in V4, checking it or not shouldn't make any difference. If, instead, you want to REMOVE it from P3D V4, you must UNINSTALL it first and, on the NEXT install, install it in P3D V5 only.
2) Addon Manager in P3D5 shows that every FSDT product I have are active but sceneries aren't in P3D5 scenery library. Do I need to run their installers too and if P3D4 & 5 are checked can I repeat the procedure (unchecking P3D4) or its better (or best or only way) to keep both checked avoiding creating an issue?
Yes, you need to run the installer to have a scenery installed to the sim Scenery Library.
And again, checking/unchecking doesn't make any difference if a scenery is ALREADY installed, but DOES make a difference if a scenery hasn't been installed in that particular simulator yet.