It's a frequent question, dear, and in fact if you'll read GoddessDustyGold's "calling all switches" thread, you will see the same question there as part of her general set of inquiries about how to incorporate switchy persons into her household.
Because I am feeling chatty and do not take offense at redundant topics in the way that some on this board do, I will give you essentially the same answer I gave her, but possibly with more detail, because I'm not answering eight or nine other questions in the same post.
How an individual couple deals with both parties being in the mood for the same thing really depends upon the dynamic of their relationship. My wife and I, being in a long term relationship that has lasted for approximately ten years now, do not worry about it very much. Switching is, for us, a perfectly natural part of the overall dynamic established between us. If we are both feeling very passive and basically submissive to the other's wants and needs, we frequently just wind up cuddling together. Otherwise, if we're both feeling submissive and horny, we have sex. Being responsive to your partner's wants and needs is never a bad way to have sex, nor is the unselfish desire to give more than you recieve. The main difficulty I have is the fact that I am a masochist, and she is not, so there are times when I want a greater degree of active participation than she is willing or able to offer. However, I am a patient man, and I know that my turn will come. I can wait a few hours, days, months, or in one case that I have mentioned somewhere on this board, years for my turn on the bottom. I am far more concerned with the wellbeing of my partner than with any selfish need for a particular sort of playtime.
By contrast, if we are both feeling aggressive or dominant, we simply get into a wrestling match. Actually, we frequently dice for it, since we're both gamers at heart. We have been known to wager sexual favors on the outcome of some battle between our characters. Just as often, we simply struggle to pin each other and hold them still long enough to get the cuffs on and the ropes tied. Some times I play to lose, simply because I enjoy a good attitude adjustment. The rest of the time, I tend to win, simply because I have a few basic physical advantages over my wife that make it easier to pin her and hold her immobile. (Also, I think she plays to lose as well, and does so far more often that I do). Because we're gamers, there is a strong roleplay element in everything my wife and I do, and we will often establish a scene by first defining who we are and what we can do. Very often, these new personae are far more aggressive than we would be if we were simply being ourselves, and so we avoid the stagnation of a long-term relationship by constantly being in a position to try new things. Being someone else is great for that, since some times a thing YOU would never try is perfectly natural for THEM. I remember once spanking her with the flat of a broadsword - there was something I never expected to include in the toybox. I'm just glad we have one without a real edge (although using one of the sharp ones to cut the clothes off of her was fun, too. Knife play can be a real thrill as long as you're careful about it).
Mutual switchiness can be a bit more difficult in short-term relationships. Some times, you go to a party or out on a date expecting to be one thing, and you find you just haven't got it in you for whatever reason. If your partner is a switch too, you can usually just negotiate a different scene, but if you're both in serious sub mode, some times cuddling is all you can do. Of course, there is always the option of finding a willing third. Two switches in dominant mode attempting to assert alpha-dominance by out-abusing some poor third-party submissive can get pretty wild. It gets pretty wild with two dominants of any stripe, but I've found that frequently it's the switches who push the hardest, as they have a clearer understanding of what a submissive really can do and still have fun doing it. Besides, it adds a competetive element for the sub, as well, with a pair of unsympathetic tops who both can sneer, and in perfect seriousness say "Is that all? I've taken worse." It's been my experience that "pure" dominants frequently back off early, rather than go too far in a scene. Lacking the basic ability to empathise with their victims, they haven't got as clear an understanding of how far they can really push before hitting the breaking point.
The key component of any relationship of course, is compromise. I have never seen a situation where two switches could not come to some sort of an agreement, even if it's only to the tune of "I will gladly whip you tuesday for a buggering today"
Think of my verbosity as a sort of litmus test for our relationship. I write in a manner identical to how I speak and how I think. If you can not cope with what I have written here, it is probably for the best if we go our separate ways.