Blue pencils are used because photocopiers didn't used to pick up blue. This way you didn't have to worry about your sketches showing through.
Now, we don't photocopy our pages anymore, we scan them. This means you can pick whatever color you want to sketch with, as long as it's different enough so you can tell your computer to ignore it.
If you are using a light table, why don't you just put your sketch under your paper and draw right over it? That's what I used to do, I just inked straight onto the paper. That way it's a total non-issue.
You ink on top of non-photo blue pencil the same way that you ink on top of regular pencil. You just do it.
The whole point of non-photo blue is that it doesn't reproduce, so you don't have to worry about clean erasing. Just draw as darkly as you need to be able to see your lines, and if you can't erase it very well, who gives a shit? It'll disappear all the same when you repro.
Yes, you can use non-photoblue with a light table.
I ink over my non-photo blue roughs. I love it. I've been using it for over fifteen years, so I'm fine-tuned to it. I sketch out the whole piece, and then I use an eraser to make it lighter where needed. Like anything, it just takes practice.