As Leen mentioned, null philters are your friend especially for exclusive pet projects where you are almost guaranteed to have unwanted vis traits that will definitely get passed on. The important thing to remember is that the only restrictions on breeding is on siblings/half siblings. Everything else is free game and if you have limited pets, you'll need to use them all to the fullest.
It can be very disheartening at the start of a project when you are hatching offspring with one or two carried traits, but it will get better! My
Dark Fairy Fae is in this painful beginning stage, but I know if I just keep breeding I'll wear rng down and make some headway. :-P
I keep my projects limited to one stable tab, but others will use an entire stable. You'll have to see what works for you. I find I get too overwhelmed so I have to limit myself in order to force myself to release the lower trait offspring. But, I also have multiple projects going at once.
Technically you only need two unrelated males, but I find it better to have a few more in order to cover different traits. Like one of my male faes has g2 and m1 another has g3 and m2 and yet another has g1 and m1.
It looks like there is a male on AS with fallow deer set for public breeding. Unfortunately, it has a hidden but hopefully you can breed a female with nothing in that slot and eventually get the fallow deer.
Hope some of that is helpful, and good luck with your project!