The best you can do is keeping them separated and pair them with other units of the same gender. Of course that won't be the case now for Fates due to confirmation of a homosexual relationship.
Ah Inigo. <3 I wanted to marry him in my last awakening playthrough. But I kind of forgot I hung out with Chrom a little too much. So that awkward moment I ended up marrying Chrom. :c
Lucina in Awakening and possibly Aqua in Fates. I couldn't marry Lucina, because it would be really awkward for me due to the existence of baby Lucina. My male bae in Awakening would be either Henry or Ingio, and in Fates it's Harold/Arnold.