Your concerns are very valid and you are very wise for addressing them in advance. Wow, I really don't know what to say here. When you are bringing in a new dog, expecially into a home where you alredy have a dog, it is so important to be able to get a feel for it's personality and how he/she will adapt and also how the dog you have will react. Ideally, I'd even say staging a "meeting" between the two and seeing if they will accept one another before making the final decision to bring the new dog home.
I can't imagine having to decide on a dog at only a few weeks old
without having to take into consideration the one I already have. Having to factor that in only makes it more difficult.
Surely the breeder understands your position?
I would really suggest letting the other interested party select their dog and really evaluating the siutation when the other dog is older to determine if he/she is a good match for your home and NOT concretely making a commitment on either at this point.
I understand your concern about marking. And even with two neutered males, they are still territorial and are likely to act as such. For that reason, I would suggest the female. Irregardless, given the circumstances, I would think that marking should be the least of your concerns at this point.