well ya dont necessarily need pro image editing program, mine skills in paint beated shadow's skills in ps like 2 years ago exactly on this matter
but yeah ps or some other editing tool that comes with scanner makes it much easier, with ps it shouldnt be any trouble, and gimp is best image editin tool out there and its free but yeah it is a bit more complicated to use
idk how scanner itself would influence in bad img scan, never had any problems with mine so idk
general thing ya would want to do is to play with contrast a bit, i dont think there would be anythin more to do, but if there are problems ya might want to try turnin it into grayscale and then adjustin its levels, personally me didnt had many drawings myself and didnt needed to make transparent bg for them (except that one occasion when me did it in paint), but this should be how it goes
since me assumes ya will be usin adobe ps
grayscale is found at [b]Image - Mode - Grayscale[/b]
to adjust its levels go to [b]Image - Adjustments - Levels[/b] (moving sliders one towards another decreases span of color tones and that way it increases contrast so to speak)
and contrast is also found in [b]Image - Adjustments - Brightness/Contrast[/b]
although ya already got advices on drawing techniques, which aint mine field really, me still thinks that regardless of drawing technique its always possible to pull this up correctly with computer tools
so play with it a bit, hope it helps