No problem, lets say your injecting 1CC of each.
1- Pull back to 1 CC on plunger.
2- Poke first bottle, inject 1 CC air
3- Draw back 1 CC of fluid, Withdraw
4- Point pin up, pull back plunger to 2CC mark
5- poke second bottle (remember pin up) inject 1CC air.
6- Draw back to 2CC mark.
You should be golden. A little mixing of fluids in not going to hurt anything.