So many times in our games I'm having the ship maneuver tool overlapping existing ships and squadrons - any rules on this it's almost impossible to keep items in place even clicking unused portions. I almost feel like I need to buy more rulers and make shorter sets

Any thoughts?

Buy an extra ruler and only build the initial segments.

Or right now mark things that can be removed and remove them. Squadrons that's always easy enough. Ships as well. Simply line up a straight line to mark the angle and front of the Ship.

The tournament rules provide rules for how to handle this:

It may be necessary to move a ship when the maneuver tool cannot be directly placed onto the play area due to the presence of other ships or squadrons. When this occurs, the ship’s owner should determine course, then hold the maneuver tool above the activated ship and move it to its final position. Both players must agree on the ship’s final position and facing. When moving this way, the player cannot adjust the maneuver tool once he or she has lifted the ship off of the play surface.

In my casual games, we've just been picking up the squadrons and then putting them back down, making sure to maintain the intent of the original placement (i.e., if they were just outside engagement, be careful to not make them engaged, or simply don't count them as engaged once they get put back down). For ships, we're a bit more careful, and make sure to respect ranges.

I've seen people say they use the "L" shape punch-outs that came with the core set to mark positions of squadrons and ship bases and then remove them out of the way for the measure tool.