Separate them out immediately.
Geese will begin pairing up as early as November and will continue to decide who should be with whom during December and January fights to show off their bravado. While you could probably separate them out later on, there's a good chance that some of the geese will have paired up with the wrong breed. At that point it's very difficult to get older geese to pair up with someone else, and some of the younger geese will fret all season, too. As long as geese are within hearing distance of one another they will still call to their chosen mate.
Throughout history geese have been called Valentine's Day layers, since they usually will start laying in mid-February. The weather and artificial lighting plays a role, as well. And some geese just want to lay early. My flocks will usually start laying sometime in February, then I begin seriously gathering the eggs two weeks later. The first two weeks' worth of eggs are the only ones we get to eat and use for crafts. After that we're hatching and selling.
I have already separated out my American Buff and Pilgrim flocks early. They will remain separated until around April or May when they stop laying eggs. After that you can put everyone back together again in a large flock. The breeds will all hang out together, but will still segregate themselves a little (the Buffs will all be in their own cluster near the same grazing patch as the Pilgrims). Keeping a couple of breeds of geese isn't a big hassle if you have two pens. To free range just alternate the days they can go out or set up a fence that keeps them separated.
Also, I had a hard time identifying the male Pilgrims from the Embdens. Some Embdens were noticeable larger, but some of them were Pilgrim size. Since male pilgrims look very similar to Embdens it was hard to tell (in fact, I started out with 2 male Pilgrims and 6 embdens. At the end, I could only positively identify 1 of the Pilgrim males).
This should never happen between the two breeds. There should also never be any mix up between Toulouse and Pilgrims. Embdens are supposed to be _much_ larger than Pilgrims and after their first molt are snow white geese. There should not be a speck of color anywhere on them. Pilgrims are a small to medium goose - in fact, the UK has them listed as a light breed along with Chinese and Romans - they really do hover the line between small and medium geese.
Pilgrim ganders should never be snow white. Ideally, they should have a grey saddle on their back that is concealed by their wings, but it is very difficult to get ganders that don't have grey on their wings and tail. So the general rule is that if there are light grey feathers on the backish area, that will be a Pilgrim gander (or a sex linked mutt goose, but we won't get into that
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