I learned this the hard way. You really need to sit down and plan things out in a spreadsheet or on paper first. I would plan a flight and then realize that the subsequent flights took up too much time so I would move everything this way or that not realizing how much I was spending to do so *embarrassed*
I do this with various browser tabs.
The first tab is always the "Schedule" screen.
The second tab is the "Open New Route" screen that lists all the destinations.
And then whenever I find a route I want to open, I open a new tab for each destination.
Then I work left to right across the tabs as the flights progress per day. That way, if I get to the last tab (be it the 2nd, 3rd, 4th flight, whatever it may be that I can fit in a day) and it won't fit, I just go to the other tabs and tweak the turnaround time in order to get everything to fit.
And then ONLY when everything fits, I submit all the flights. Then I go to the Schedule tab and add them all onto the respective plane. When everything's scheduled up without error, I delete all those flight tabs (don't delete them before, so you can easily Edit them if you made a mistake since they're still right there on the tab), then repeat the process for the next plane.