Looking into colour harmony will help overall with understanding colour working together.
A lot of it is also experiment and practice.
I personally tend to use either a set of microns to line or a technical pen filled with india ink.
lots of inks will bleed depending what you use for colour though. If I'm using my copic markers I have to line afterwards otherwise it tends to bleed and look mucky. Pencil crayons (I like prismacolor premiers) I can line first, but usually still better to line after so they look dark and crisp.
Any photoshop will work for taking pencil to PC, just switch your lineart layer to multiply and you can colour under it.