Where do we start. You need a good breed, or a dog good and willing to train. Sounds like you got that on check.
Lets start with you question. Keeping them from getting gun shy. I have a dog that will tree squirrels, opossums, and coons but you bring a gun out and he will run the other way. Sometimes you can't get it out of them. But you can do somethings while they are young to help them get use to the sounds.
When they are pups, shoot blanks, .22s around them. When you are target praticing make sure the dogs are around. Shoot, and praise them, give them a treat. When you go and feed them, take a pan and a spoon and hit it while they are eating. If they are hungry they will ignore the sound.
For me I hunt mostly fiest. They like to use their eyes and ears more than anything. So I take a squirrel tail on a fishing pole and play a game with the dogs. I start this at 4 months old. Make the tail go up a tree and see if the dogs will bark at it. Make them chase it, have fun with it. Then if they bark, shoot a blank or .22 and let the tail fall. This will get them in looking for something to fall when you shoot a gun.
A cur or bigger dog may not react the same way.
Really it takes alot of time in the woods. It took me 3 years on one dog and 2 years on my other one to really get them treeing. Some people will dissagree, but it takes 2 full hunting seasons to see if a dog will turn out to be a dog. Some start early and some start late.
2 dogs to train at one time maybe a task, when both are pups they may just want to play and not hunt. You will need to take them out one at a time. Then later on when they start treeing you could take them out at the same time. I like having my dogs years spread out. I like having an older dog treeing, then a year or two later get another one, then in another year or two get another one. It helps when the older dogs are treeing and the pups see the squirrel fall.
NEVER! I mean NEVER EVER EVER EVER! Shoot a squirrel out to a dog unless it barks! My black and white dog would not bark up at a squirrel, but would put it's paws out on the tree and wait until I get there. I shot the squirrel out thinking she would start barking. She never did, until I tied her back on the tree and waited until she barks. Now she won't shut up on a tree! that was the biggest mistake I ever made. I wasted 2 good years out of her. Nearly gave up.
I can go on and on. I hope this helps.