All you need to do is tie in anywhere between the city water source and your manifold (where all the valves are grouped). If the valves are not grouped, then you just need to get to the source side of any valve, because logically they are still all connected on the source side.
The other thing to keep in mind is that your pipe doesn't HAVE to go in a strait line. You could cut a zig-zag path through the trees trying to stay as far away from the trunks as possible. It will be a lot more pain, but it's an option.
Another possibility is to not dig very deep and do your best to stay away from the base of trees. That way, you only kill a few surface roots. Normally this wouldn't be a good idea as the line for someone on city water would be under constant pressure. But your system will only have pressure when the pump is turned on, and then worst case you're wasting electricity running a pump thats sending lake water to a leak (and presumably running back down into the lake). Of course the shallower the pipe, the more likely it's to get damaged. If you're running a low flow system (say MPRotators) you'd MIGHT get away with 3/4" copper pipe, or use two sets of pipe (sleave the main pipe inside a larger "protection" pipe). But that can get $$$.