It doesn't have to be tedious...no, 0,0 is always 0,0...it is very easy...no...yes.
Now that all of the short answers are out of the way, lets go into a bit more detail.
Starting with placement, you can place the holes anywhere and move them in the Constraint Manager. The locations there are a little easier to grab hold of--1" from left, 1" from top instead of a static distance from 0,0. You just have to apply both constraints then edit each with the location you want. The hole will then stay at that location no matter what size the cabinet is.
You do the same thing when using an extended tool file for the hole patterns. Apply it, cut the holes, constrain the holes then edit the constraints to locate the holes exactly where you want them. It sounds like a lot of steps but it really takes only about 2 seconds to perform. The first few times will take a little longer of course, but after you see exactly what is going on, you'll be amazed at just how quickly you can do this.
Using this method, it doesn't matter what size the new cabinet is. You simply set the constraints to keep the holes where you want them.
You can easily keep from needing to modify cabinets by creating a new seed library with the holes and constraints in place. From that library, use whatever seed you need to start with, modify it and save it as your new cabinet--complete with holes and constraints. You can then resize it and the holes will stay where you want them.
Creating an extended tool file??? Simple!!! In Contour Mode of the Part Editor, after defining but before cutting the holes, click the save (diskette) icon on the bottom toolbar. Browse to your profile tools directory, name the file and save it. Next time you need it, open it (make sure you select .x_t as file type to open) and cut the holes.

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