One of the nice things about such fixtures is the ability to change your mind later on.
What I'd do is if I wasn't sure, I'd mess around with 1 in 3 channel mode and 1 in 28 channel mode, either at gigs or on your own time. See what you like. Then try both one way and both the other, and again, see what you like.
I do strongly back Jingle's suggestion about going with a software controlled platform unless you have the funds to go for a rather full featured lighting desk.
There really is no best way to answer your question. Screw around with them and figure it out. In my similar situation, I hvae 4 Mega Panels. I've chosen to go wiht 7-channel mode, it works best for me. In fact, currently, all my LED fixtures are in 7 channel mode. The consistency and how I use them, this is a ideal match. The Mega Pane I think has a 26 channel mode, but for me, especially with how the default profile is(but mainly how it works), it's just not something I will utilize, at least not for a while.