Been a few years since I did anything like this but, if you have the printed originals, I’d aim to get as clean a scan as possible to start with - play with the brightness and contrast at the pre-scanning stage for best results. You may also get better results if you put a solid black backing behind the originals, as that will help keep the contrast consistent across the entire image.
I’d also tend to work in pure black and white rather than greyscale, so scan at 1200ppi, ideally.
What I used to do was create a new layer for colours, below the linework, and set the linework layer to Multiply. That’s not ideal, though, particularly if you’re working with greyscale scans. Much better to work with transparent 1-bit/bitmap - wide areas that want a single colour, you can use the magic want on the line layer, switch to the colour layer, then fill (possibly expanding the selection by 1px first). Other than that, colour by whatever method suits you best - hand-painting if you have a tablet/stylus can be a lot of fun… Not so much with a mouse, though.
If you end up wanting to colour the lines, make sure to switch on ‘Lock Transparent Pixels’ in the Layers window.