The way I do it is having x/y endstops at one end. These are my reference 0’s because they don’t change. When I do parts that require multiple bits I make sure their 0 is always in the same place on the files. Then I do the following;
1: Attach whatever I’m cutting to the spoil board.
2: Load the first gcode file.
3: Hit X and Y home in repetier, this brings the router for me all the way to the left and front.
4: Jog the router over to where I want the new 0 to be.
5: Use my homemade touch off plate to set Z 0 by hitting Z home in repetier.
6: Write down the current X/Y position on a postit note. <<<— This is my Achilles heel. I forget this part way too often.
7: Hit the Set 0 shortcut button in repetier to set my new 0 at the current location.
Once it’s done, I just swap out the bit, which usually moves the router, so your 0 is now gone, and start over at step 2 with the new gcode.
The easiest way to size parts in Estlcam is know what size they were in whatever cad/cam software they were designed. Then when you import them, use the same measurement system. Otherwise I just change the grid size to a known dimension and scale off that.