Q1: I think it is not a real problem when trains are not perfectly spaced, as long as they do not all group up in one line. In your setup (double track, 4 cities, 6 trains) I would use no signals, and let the stations do the work. They have invisible signals. The only 2 signals you need are at both ends of the line where the tracks come together to the one platform of both end stations. Destroy also all cross-overs left in your double track at the other stations (left-overs from a growing line). They are not needed, and just give potentially path problems. Until we have waypoints and alternative platform usage, I believe this simple setup is the most effective.
Q2: In real life it is a common to use fly-overs to cross 2 double lines outside a station, so the trains do not have to cross each other and switch tracks in the station itself. If you do not have the space for a fly-over, you have to cross the lines on level, with points. And since we do not yet have crossings or slips, crossing lines on level is rather cumbersome and a hinder for smooth train traffic.
But these are just my preferences. There is no “best” way. And a part of the fun is solving the puzzles. 😉