what is the best way to re-route multiple parts in same package and choose connectors with Diptrace
Sure, this is a pretty standard feature in a lot of PCB design packages. It's generally referred to as "Back Annotation." While I haven't used Diptrace, both PADS and Altium Designer provide this feature, though I used it very sparingly.

According to the Diptrace FAQ:


  If you have made changes in PCB, use Back Annotate feature in Schematic (select "File \ Back Annotate \ ... " from main menu) to bring changes from the board into the circuit.


This should update your schematic with the changes you've made while routing the board.

The key is consistency. If you're not diligent about updating the schematic to reflect any changes you've made in the layout, then it's pretty easy to get lost.

I will also say that I've tended to use forward annotation (updating PCB with schematic changes) more than back annotation simply because it seemed to be easier for the software to handle, but it's definitely worth a try. Just make sure to back up your board files first!