I have a standard proceedure for all my new goats under a year of age. All of this stems from a purchase we made from what we thought was a reputable breeder, introducing a strain of cocci my goats had never been exposed to into my herd and killing two kids (and the buckling that brought the cocci to us to begin with). It not only cost us in terms of loosing investments and expenditures related to vet care...it broke our hearts.
So...all new goats under 1 year enter a 21 day quarantine. They are placed in 10' x 10' pens away from (but within sight and sound distance) my herd. They all go through an intensive deworming program (2 dewormings with 2 dewormers 10 days apart), daily cocci treatment with either Albon or Amprollium, and a two series course for C/D & T. During this period, they also recieve large doses of ProBios to keep their rumens happy despite all the antibiotics (just note that you can't give the probiotics at the same time that you drench the antibiotics, the meds will kill the probiotics, too). Only once all of these treatments are complete are they introduced to my herd.
The primary downside to this is that if you aren't getting more than one goat from the same place, they'll be alone and therefore be stressed.
I speculate that IF you do cocci treatments (as indicated for treatment, not for prevention) you should be able to keep your girls together from the get-go because they'll both be getting treatment and shouldn't become ill. IMHO, with young goats your main concern will be different strains of cocci that they haven't yet built immunity to.
Also, be sure to get some feed from each breeder to graduate the kids onto whatever you'll be feeding.