I think you’d be making it very difficult for yourself if you try to train both at the same time. You can train one rabbit but not the other (to the other rabbit, the one who doesn’t get a reward, the clicker will mean nothing), or you can train both if you train them separately.
The crucial part of clicker-training is the timing, the clicker means “well done, treat on its way”, and the animal must be given a chance to realize what makes the click-treat come. And even if you can train animals to do a series of tricks, all in a row, that’s not how you start out. First the animal must make the connection between the desired behaviour and the click/treat. If the click-treat comes even a moment to late or too soon, you make it hard for the animal to know what you mean. Obviously, if you only reward the one rabbit, the other one isn’t really given the proper opportunity to get what it’s all about. Kind of like “Click, and then HE gets a treat. Yeah, that’s a fun game. Not.” I think either the other one will be too interested and interfere and fight for the treats, or it will turn its furry little back on the whole project.
But if you can do sessions with them separately, I’m sure you’ll have lots of fun with it. It’s very rewarding.