My main things, I don't fixate on clean lineart (and therefore I can't rely on paint bucket because I literally can't use it xD) I do a thumbnail sketch, then a cleaner sketch, and if the second sketch is still like super rough, I'll do a third one, and then just manually start painting under the sketch. I personally feel that perfecting the lines just slows me down when I can hide most of the bad lines through painting.
Also, the one that is a little more out of the norm, I paint like 90% of things in one layer (usually bg would be separate, and then after that it's like little details or stuff I'm not sure I want to add to the painting, but skin/hair/clothes?? All that, one layer). And then debating if I want to keep the lines or stick with more painterly, I will actually merge the lines into the painting layer and paint over them with a hard but still blendy brush (the Poketober stuff I merged, the recent icons are keeping the sketch/lines). But anyway, because I use brushes that blend/have opacity, I find that using one layer to paint with a blendy brush really helps unify things for that painterly look. I'll on the occasion use filter layers but for the main paintings I try not to rely one them. In your case, if you are using multiple layers, maybe erasing the edges with a soft eraser can help with the painterly stuff a bit?
In terms of colours, like I mentioned, since I don't rely on filters (so no multiply or overlay), there is a little more freedom in picking different hues and going a little more wild.. If I'm shading something, I change up the colours of the colour wheel vs just picking a darker/lighter colour (so say I was painting something red, instead of picking a red and moving downright in the colour square for a darker red, and upper left for a lighter red, I will move the wheel to a purple for the shadow, and to an orange for the lighting). And then once you have a sense for it it's a lot easier to just shade in completely random colours.
What program do you use? I am team basic so I use Sai 2 and my main brushes these days. These are the main ones I use, incase you use SAI 2 I can give you the settings. ^^ The top three are my main brushes, and the airbrush is only ever used when I need a soft blend (like adding a gradient), but otherwise avoid it like the plague. If I wasn't too stupid for sai I would love to insert custom brush tips, but I literally couldn't do it even with a guide so I'm stuck with the defaults, and kinds settled into using a circle brush mainly. ^^'
I hope this makes some amount of sense, if something is confusing let me know and I'll try to clarify it better. ><