I haven't tried any of the auto-group setups for raid. I manually invite the group leaders and accept, since it's just a quick click on each guy. Then I have the raid window open to set the MT and master looter anyways.
Loot - I would suggest making sure you set your raid master looter to one of the group's master looters. I've had the auto-looting things stop working when I go raid-mode sometimes and I'm not always able to figure out why.
Healing outside group - I'd setup your healer to cross heal the other group's tank.
KA has extended target healing built in and it is easy to setup.
Pulling - Not much point in running more than one puller. KA's pull routine will stop a puller mid-pull if it sees more mobs appear on the xtarget window. You can run chain pull mode, which will go for more mobs once there is only one mob alive. I've also run two pullers, each set to opposite 180 degree arcs (via [Pull] settings) so one guy ran east and the other ran west. Whichever found a mob first won, so it was a tiny bit faster.
MGB buffs - You can add "|mgb" to some group buffs if you have the tranquil blessings AA. KA will mgb them if you're out of combat long enough and the buffer has lost the buff themselves. The "out-of-combat" part is the tricky one, it's quite a long wait at like 30 secs. I set a longer pause in my puller's Pull section so they'll check every 30 mins. I've gone back and forth on the usefulness of using MGB. It's great to have fully buffed raid, but I don't like editing my ini every time I go from raid to group setups. Maybe a raid-version ini would be a better way.
Tank target selection - I ran all tanks in Tank mode. They'll choose their own targets, so sometimes they'll be on the same mob but usually they'll select their own. Once in awhile, it seems like one tank would decide the other tank "had the mob first" so KA's anti-KillSteal code would stop the tank from attacking. Doesn't happen a lot, but I did notice it.
How to assist - Mainly I just let both groups assist their own tank and let the tanks sort out who they want to kill. If named shows up, all tanks will attack it assuming you have them with Burn turned on. At some tough camps, I did have a few other-group DPS set to assist my stronger tank. I figured that tank was most likely to survive a bad pull and wanted any DPS focused on his targets first.
Mezzers - You could run just one and have the other groups mezzer run a pure DPS ini. I usually let all mezzers just mez, it didn't seem to cause any issues.