I'm pretty basic when it comes to digital inking, but I DO use a Cintiq, which makes things a lot easier on me. It's like drawing on paper, only it's digital.
Here are some basic tips that work no matter WHAT your setup is, though.
1.) Inking on different layers.
You don't have to lump all of your lines into a single layer. I use 2-3 layers, depending on what I'm drawing. One layer for inking the characters, one layer for the environment, and one layer for anything that falls in-between those categories. Crowds, sound-effects, visual effects like explosions, etc. Use as many, or as few, as you need. This makes erasing and re-drawing things easier.
2.) Lineweight
This goes for traditional inkers as well; varying the width of your line, depending on what you're drawing, will help a LOT. Lines will tend to be thicker where they meet, or where a shadow might fall, and thinner on small details, and on edges facing the light-source. If all lines are the same width, your inking can come off looking stiff or kind of cardboard-cutout-y. If this is the look you're going for, though, go ahead!
3.) Tools are your friends
Let's be honest; a lot of us have issues drawing longer straight lines or curves that don't come off looking shaky or weird. Embrace the pen-stabilisers and the line-tools (which in Manga/Clip Studio 5 at least have lots of variables and sliders that can make them look less artificial!) and work with them. Using the line-tool might make a stiff and boring line, but there's nothing that says you can't go in afterwards with a brush and tweak the line to make it look more natural.
