In general, the person who does the most work probably gets first say. Maybe they get first pick of their half, or the other person picks a couple and the breeder gets more than half. It really depends on what you're both looking to get out of the loan (bloodline, best looking baby, baby-sales?). It is extremely important to talk it out beforehand - explain what you're hoping to get, listen to what they're hoping to get, and try to reach an agreement. Don't leave it up to the babies being born and you're both fighting over the prettiest one. Everything should be laid out clearly, and if an issue arises talk it out like rational adults.
I'm currently doing loans with two people - Katrina has my female merauke in the hopes that she manages to breed (we share the goal of each having a great group of meraukes one day, but right now we're working together to increase the chances of success - teamwork!). And I have a female northern from Sheslikeheroin (who has my female kingsnake to breed) - both of us are interested in having some different babies to sell (since neither has a pair for the animal on loan), while also wanting the chance to diversify our breeding bloodlines a bit. I've also done a bloodline trade with Pink T. Monkey to give fresh blood to both our breeding groups.
Trades and loans really can be fantastic for you - but make sure you're doing them with other great people. Don't just throw two skinks together for the heck of it - have a reason and plan. Working together can be more rewarding that I can say - it's a community
How cool.