So I've just been playing around in the Design Lab, and it looks like EE AtAt creates Seal Bay. So I'm guessing if both horses are EE AtAt then the foal will also be Seal Bay. 

In the wiki it says:
In combination with at least one extension gene agouti will make:

• A+ – A+ is the gene that creates Light Bay horses.

• A+A+ – Two A+ genes creates Wild Bay horses.

• A – A is the gene that creates Bay horses.

• At – At is the gene that creates Brown Bay horses.

• AtAt- Two At genes creates Seal Bay horses.

• a – Horse will not be bay.
   

  The wiki says ‘a’ will not create a bay. But I've got a Brown Bay mare who is EE Ata Zz. So if I create this custom stallion who is EE AtAt ZZ, will the foal be a Silver Seal Bay if there are no diluting genes present?

the agouti works in a hierarchy which is why its in a list form like that, the “a - Horse will not be a bay” means horses with aa not horses like A+a, Aa, Ata, etc.     

Ahh okay, so will it simply depend on whether the foal inherits AtAt from the stallion rather than the a from the mare? I couldn't see if either of them are recessive or dominant.