1)If you had R: TW and installed BI over it, you now have 1.3 and 1.4.

2)I don't think it matters. You now have:

R: TW 1.3.
BI 1.4.

Install patch 1.5 or 1.6 to either upgrade Rome or Barbarian. I don't think it matters what's first. Personally, I installed the 1.5 patch first because I'm more of a RTW person, then I followed it with 1.6.

3)No, I don't think so. After all, they 'are' patches that does some really good work, and important changed to units (More in BI) just to balance some factions.