I'm a little confused, but I'll answer it as best I can if I am interpreting this correctly.
To share my experience -
My tap water also contains ammonia due to chloramines, usually around 0.5ppm. Of course this is still measureable after its been locked up by prime, as the standard ammonia test measures total ammonia (If I'm not mistaken). You can get test kits to measure just free ammonia, and just total ammonia. (Seachem make this).
Anyway the point I am getting to, is that the biofiltration in my system consumes the ammonia from the tap quickly, before it becomes an issue. I change around 40-50% daily and haven't noticed any issues *touch wood*. I can test my water for ammonia at pretty much any given time and it will register 0.
I hope that makes sense and is of some help to you, until an expert chimes in