I have tried doing this several different ways, and while I have found something that works for me there are a few quirks that makes me think there are probably better ways.

A simple example is a 1/2" plate with 4 holes. What I do now is draw 2 center point rectangles on the origin and dimension the two squares. I typically select the 4 lines of the internal rectangle and make the construction lines. (Note 1). Then I extrude my plate. Then I use the hole wizard and position the holes on the intersections of the inside rectangle lines (Note 2). I like this because I have one sketch to edit for changes. (Note 3)

1. I know I can not make these construction lines but then when doing the extrusion I have to select multiple contours, and since I often go back and add more and more details to this top level sketch to add additional features I have found its simpler to always use construction lines. However it gets tedious converting lines to construction lines. Dimensions can cover them etc. Is there a way to not do construction lines but not mess up your extrusion when adding more details?

2. What is up with hole wizard and picking their positions. I have tried using points in my base sketch but nothing speeds this process up. Sometimes when I try and add a hole where a two lines cross and I often have to place the hole then go back and move it to get it stick to the second line. Another thing is I have to make sure I click on the same side of the extrusion that my sketch is on or else I can't pick the sketch. Also I have to make sure and unhide the original sketch, and then hide it when I am done. Is there any tool you can use in the sketch to say hey I am going to put a hole here, and then not have to place each one individually? Are there things that I can do to make this process more streamlined?

3. I have done sketch 1 extrude, then sketch 2 for hole locations, but sometimes you can't tie dimensions like you can if you stay in the original sketch. For instance if I want to do a calculation on my second sketch that is based on the length of a side sometimes I can just re dimension that line, but I have to draw another line on top of it and then use it to create a driven dimension and then reference it for example =(length of side -1) / 3

Here is an example of a simple sketch.