Use the gravel vac to get down to the bottom of the substrate.
Add it either to the new water, if using buckets, or directly to the tank if using a python.
It's fine. Some folks don't like it because of the potential for heavy metals, I've measured tap water and not found a significant amount. That said, it wasn't your tap water that I was analysing, but most folks haven't had problems using tap water.
Edit: Although I should add that it all comes down to how much turn over your water tank has. If you've been away for a while, it's always best to run your taps for a while to get out any build up. Same goes for your hot water tank. If yours sits with the same water for days on end, then it may be an issue, if you run through a lot of hot water, then its not going to matter.