In general, the PDF has worked well for me. I usually have the laptop up and running anyway so I can keep track of time, weather, etc. The pdf allows me to bounce back and forth relatively quickly from page to page and the laptop creates a bit of a natural GMs screen.
I will; however, occasionally print out a stat block that I know I will be using in order to avoid all the flipping around in the pdf format.
For running tabletop, we printed a copy of the PDF - but then we have access to a decent printer. I write all over the module as I run it, which is an old habit from way before modules were available in PDF format.
Now I am running an on-line game, the PDF works fine for me.
I use a printed version of the pdf's for my personal notes and have a laptop with the pdf's open as well. That way I can have stat blocks and other file in front of me at the same time.
As for the maps, you can copy them without notes for traps and such with a right version of adobe reader (an old one, I'm leaning towards seven but I would have to check that when I get home). If you're using a digital platform, such as roll20, these work perfectly. I've also experimented with printing them with some mixed results.
To do this I have an Excel file which is set to be inch grids once printed (again I'd have to be at home to check the measurements, if you're interested let me know and I can send the settings or the file to you. Sadly setting Excel to 1 inch doesn't work and the grids comes out too large).
I then crop the edge off the maps so the grid aligns with the edge of the image and copy the file to Excel.
Afterwards you can expand the image to the point that the grid aligns with the lines of the Excel cells, then you can be sure it will print in 1 inch squares.
The problems with this are that you end up needing to print a lot due to the scale of some of the maps. Images that aren't roughly squares end up with a lot of 'empty' sheets (this can be solved by not printing every page, but is somewhat tedious. But mostly the problem is that a resolution is somewhat lacking when you magnify it this far. If someone knows if this is solved by using different software please let me know.
If you want an idea of how they look I can send you some photo's. I also still have some of the files ready to print which I could also send if I can still find them. Not all of them though as I run a lot of the campaign digitally. Hope this helps!
I find that if I select an image and copy it - it comes without the notes or tags. If I want the whole thing I print the individual page from the PDF - or snip / screen grab it to work on in paint.
I don't bother scaling printed maps for combat with minis - instead I bought a cheap plastic table cloth with a check/gingham pattern and draw directly on that with dry-wipe pens. I normally find one with the right size pattern on ebay and then buy it by the metre.