Hi Jake,
With smaller groups, I find that I don't always have to go with 'immediate rewards'...my groups tend to prefer to 'save up' their rewards for something bigger and less often. I teach GATE 3rd and 4th grade, and so all of my classes are small group. I admit, I miss the big groups-- there's always more energy-- but it's working out with the smaller groups.
My groups all work towards 'game time', where they get to play with some of the mind-bending and critical-thinking games I keep in my classroom. They only get 1-3 minutes each day (if any), or they can lose 1-3 minutes if it wasn't a great day. Then, when they decide they need a break or a change-up, they can vote as a group to use their game-time. So in effect, they are getting 'rewarded' every day (which I think it's important for them to see the effects of their hard work) but aren't using the benefits of their rewards every day. In fact, if they are working toward something they really want, then every time you give them a point, you are 'rewarding' them. That's the whole idea. Pleasure-- pain... pleasure, pain...pain... pleasure...pleasure...pleasure..pain..pleasure..
you get the idea. the more you bounce them back and forth, the more they stay involved.
With multiple small groups, you need multiple places to keep track of scores. I have separate boxes on my whiteboard, you could keep separate pieces of chart-paper, separate small whiteboards, or separate spaces on your large whiteboard. Whichever works for you. If you want to simplify this, simply allow them to receive their reward (or consequence) each day -- early to recess, lunch, etc... it's only ever a few minutes of the day, and allows them to immediate reap the benefits, without handing out candy, coupons, etc.... That does make for much less tracking on your part.
As for the rest...run it just as you would with a regular class. You wont get as much 'frenzy', but the learning is still happening, and the engagement is still clearly evident. The students may feel weird at first, but if you are consistent with it, they get over that.