Use the high IV Morty as the base. You can't look at IVs in the combine screen, but you can see their stats, so be sure to identify the ones for your high IV Morty and select it as the Morty you will be combining other Princesses into.
It doesn't matter what the level or stats of other Mortys is, as long as you pick one to add others into, which is probably why the game reminds you to know what you're doing as you could easily pick the wrong Morty as the base and lose the better ones if they're combined into less-powerful Mortys.
Edit reason:
(Morty) Aww geez, Rick, it's Saturday. Sh-sh-shouldn't we sleeping in?
(Rick) Shut up, Morty. Early bird gets the worm, or whatever.