Interesting technique. Most of my projects have some manifold plumbing, up to maybe a hundred holes and 8 or more lines. So this is worth thinking about.
Here's what I settled on:
Make the block transparent. Work out the paths in a 3DSketch. There's too much revision going on to monkey with cut-extrudes or HW holes while figuring out the paths. After the paths are figured out (or even partially so), I use library features to insert HW holes, with their position and depth tied to points in the layout sketch. They go in fast, and I have them color coded. Before 2005 unified the palette/library features, I had a macro to create these, called "whack-a-hole".
If I need to edit the layout, things can get confusing, because you lose all the color coding. Good ol' Dynabits RedLight to the rescue. With rebuilds blocked, you can edit the layout sketch and still see the holes. You just can't select them, since you can only select geometry higher in the tree than the layout.
I soon hope to have hole callouts in the library feature files that are inserted with the hole. This is because the hole callout tool in drawings is completely useless for intersecting holes. This in combination with annotation views in 06 could really accelerate documenting manifolds.