This appears to be a duplicate of a forum post from earlier, but the original (and its comments) have been destroyed. In any case, here is the comment I wrote on the original:

I, too, prefer to track my work on paper. However, using paper alone necessitates the kind of "double-entry accounting" you describe, and it can get really tedious.

My system evolved to use a hybrid of software and paper. I keep track of my master lists in software, but I print my context lists out on paper and carry them throughout the day. Each morning at work I manually "synchronize" the two, recording things I've crossed off manually as "done" in the software, typing up newly-added tasks, etc.

This has the benefit of keeping my lists relatively tidy and legible (until I start scribbling all over them, anyway). I also find it useful to have a master task list in one place and then only carry with me a subset of that list (the things that may be done Next).

And if you're interested, the software I use is the free online SimpleGTD. It's great for my purposes, though another solution (as long as it has the ability to print your lists) may work better for you.