How to go about separating dogs?

So my boyfriend had a dog and he got me a dog after awhile. The dog we got was 9 months (beagle) at the time and his dog was 1 yr (Australian shepherd). I am staying in my bfs house for the summer with the dogs while he is away for work. Unfortunately we have broken up and when he gets back I will be finding my own place and taking my dog (beagle) with me. How hard is this on dog's, what can I do to make it easier, etc? I don't want to separate them but it has to be done. We've had the dogs together for about a year and they have always lived together. Thanks