Why did you do a 90% change? I don't see a reason to do that much. It's great you're doing a water change but I'd say 50% is the most necessary. I prefer to just do more frequent water changes with less amount, like 15-25%.
So you already know the answers:
3. Do more frequent water changes with less water. Make it a habit, do 25% every other day for example. Treat your water before putting it in because its REALLY easy to put the water in and then walk away. If you're using a hose to fill in the water, treat it before you add the water just so you don't forget after (again make it a habit). If you're filling in buckets and then putting the water in that way, treat the water in the bucket before adding it in
The bottom line is straight tap water will hurt the beneficial bacteria. It happens, not a big deal but it might set back your tank (sounds like a new tank setup with just plants waiting for it to by cycled). Tank/water maintenance isn't glamorous and it's redundant but it's really important so don't get lazy on it. Also, if you do get on a schedule and miss a few water changes, don't go nuts and do a 90% change - you're doing more harm than good I say. Just 30% water change and get back on your schedule.