How long and how can I hold meringue before macaronage? I have high hopes (I always do) for my next batch of macarons. I've decided to do lemon and lime. I want to do half lemon, half lime. 

My stand mixer isn't perfect, I fear that it won't perfectly whip a small batch of egg whites (so I don't want to halve the recipe), yet I want two distinct colors of cookie. I'm doing the same with the filling, but that's easy.

So, my thought is to whip up all of the meringue with yellow and then do the macaronage with half of the meringue. As those are baking, I'll add green to the meringue left in the mixer, briefly whip that, and then do the macaronage on that half. Between the two sessions of macaronage and piping, I suspect I'll want a break.

Can I do that? Is two hours too long? Should I cover it in the meantime? Any other hints or caveats?

BTW, I don't intend to flavor the cookie part at all (or very subtly with lemon oil); the lemon and lime flavor will be pronounced in the filling.
I suspect you'll be fine. I often do simple unfilled baked meringue cookies and at least some of the recipes suggest letting them stand for several hours before baking. I've tried it both ways and notice little difference - but assuming your macaron cookie part includes a substantial amount of sugar, my evidence says it should be very stable for the course of a couple of hours.