There really is no problem in doing a 75% or 90% water change. As long as you're doing regular water changes, the parameters in the tank should be similar enough to your tapwater not to cause shock.
The bacteria that you're trying to cultivate in the tank (the cycle bacteria) are mostly on the hard surfaces of the tank and on the filter media, not in the water, so removing water only removes the bad stuff.
Try to keep both ammonia and nitrites below 1.0ppm. If the fish are looking stressed (gasping at the surface, not swimming much, looking pale or washed out), it's probably time to test and do a water change.
The height of those spikes will depend mostly on how many fish you have (and their size) versus the size of the tank. The more heavily stocked the tank, the more water changes you'll need to do.