Hey there!
I started out with Sketchbook and Clip Studio and now use IbisPaintX
First off, getting cleaner lines is a product of patience and a stable hand. Turning on stabilization is also good for smooth linework. To color, make a layer underneath your lines and color away. I personally use a grey base and clipping layers, and color on top, using the fill bucket.
For simple shading, make a layer underneath your lines, but on top of your color and set the layer blending mode to multiply. Choose a darker, saturated color for your shadows. Stay away from greys, unless the charater you're drawing is greyscale.
For simple lighting, make a new layer above your shadows and under your lines. Set the layer mode to add and choose a light, saturated color.
Keep in mind your lightsource and how light interacts with different surfaces and textures. Play around with filters and brushes a bit, experiment. There's no such thing as bad art, its just another step to reach your goal.
Feel free to PM me for anything art related!