Planning the spay and neuter for about 6 months is a good plan, you do not need to worry about them breeding if you stick close to 6 months. Extracting any retained temporary teeth at the same time is great.
Vaccination schedules should not be altered for small dogs. The principles of immune system development and disease risks are not dependent on size. There are now some manufacturers vaccines prepared with small dogs in mind, check with your vet.
Water restriction is hardly ever a good idea. If you feel your male puppy pees more than expected compared to the female you may want to let your vet know and they might suggest a urinalysis to be safe.
Glad to address your questions anytime!