Oh, 521collective... I know how you feel! The Sheltie puppy we had when I was a kid was housebroken in an instant. My current Sheltie... not so much. Shelties are very smart dogs, but even so, some are tougher to housebreak than others. But don't be discouraged. This doesn't really sound like territory marking to me, instead I think it's more that 9 weeks is still very, very young, and accidents are just bound to happen.
One of the puppy training guides I consulted (it was actually the DVD that came with our crate from Midwest Homes) said that as a general rule, puppies can be expected to "hold it" for as many hours as they are months old, plus 1. So, for example, your 9 week old puppy is just over 2 months (8 weeks), so he should probably be able to hold it 3 hours. Again, that's the general rule, and every dog's going to be a little different.
One of the things that the various puppy guides (and other folks on the forum) suggest is to take the puppy out after every change in activity (immediately after eating, after playing, after waking up from a nap, etc.) and to give the puppy only a couple minutes outside to do his business, and if he doesn't do it right away, take him inside and put him in his crate, and try again in a few minutes. Once he does go, then you can let him explore the yard, play with the other dogs, etc. But that's a reward for going potty! If he doesn't go potty, he isn't allowed to play out there! Otherwise he is likely to forget why he went out there in the first place, and when he comes back inside... woops! And, again, if he's had a rollicking play session outside, then before bringing him in, give him another chance to go (since that counts as a change in activity).
Speaking of rewards, if you aren't already rewarding him for pottying outside, do so. When he goes outside, heap praises on him and feed him tasty treats. Throw a party for him! When he goes inside, do not punish, or scold... put him in his crate with a tasty treat and clean up the mess (preferably where he can't see you) with a good enzymatic cleaner. If there is any trace of urine smell left behind, he may keep peeing there because that smell tells him it's a designated potty spot.
As for the issues with his crate... SammysDaddy gave some great advice, by giving your puppy a special treat each time he goes into the crate, to help make it a more pleasant experience. Another thing you can do to help him enjoy his crate more, is to feed him in the crate.
What kind of crate is it? A plastic one that the puppy can hardly see out of, or a wire crate where he can see everything going on around him? Some dogs really prefer one type over the other. We got a wire crate, because we wanted the puppy to be part of what was happening around him, and we reasoned that we could always throw a towel or blanket over it to make it more like a cozy "den" if that's what he seemed to prefer. If your crate is the hard plastic type, try at least turning it so that he can see you... it may be that he feels too isolated in there. If it's a wire type, try putting a blanket over the top and 3 sides and see if that helps.
How big is this crate? You really don't want the crate to be too big for the puppy, because if it is too big, that will invite accidents, because the puppy will use one end as a potty spot, and just hang out in the other end. The crate we got had a divider that came with it, so we could let the crate "grow" along with the puppy. He should have enough room to turn around and lie down, but not much more. Also, if you've got a puppy pad or crate liner in there, take them out for now... they actually make it MORE likely that he'll pee in the crate, as there is something to absorb the urine and he won't have to sit in it afterward, so there is less incentive for him to hold it.
Hang in there... I know it seems like he'll never get it, but trust me... he will! Just in time for him to "forget" it all during the adolescent phase.
