For my bases I like to fill bare patches with texture paint using GW's "M Texture Spreader" - basically a tiny plastic spatula. It's a bit flexible, which makes it work easier than like a knife or metal sculpting tool, while being firmer than a paint brush to make it easier to spread the paint around. GW's texture paint is fine but pricey and gives a more grainy surface. AK Interactive's texture paint comes in a variety of surface qualities and are more cost efficient in a larger tub - though drying out is an issue, so I use some plastic wrap pressed down onto the paint in the tub to cover it before screwing the lid on when I'm not using it, and I stir it up with like a popscicle stick or whatever before each use. With texture paint you can build it up in layers if you want it to be thicker so long as you give it time to fully dry. You can also sprinkle patches of fine slate in while its wet or press in some skulls or whatever for extra texture variety or additional details - though it's a good idea to apply a spot of thin superglue after its dry to hold bits like that in.
I like to apply texture paint before painting, but usually after gluing the model on, though some complicated models are better painted separately if it'll be easy to see under them but hard to reach with a brush. Then I just paint the base as part of painting the model, and apply additional details like grass tufts or snow effect at the end. other people prefer to paint the model first, then do texture paint - picking a color that starts close to what they want the basing to be, and either leave the texture paint as is or wash or drybrush over it for some extra depth while being careful to avoid the painted parts. With something like your green crystals you'd probably want to go with the 'paint first, then glue crystals, then texture paint' order.
I like texture paint because its relatively quick, easy, and consistent, and a grainy texture especially (like you typically get from GW's astrogranite or devlan mud) is easy to paint with washes or drybrushing. But there's tons of resources on basing methods out there, including no end of great youtube videos. I like this one for more naturalistic basing using pva mixes, plus it shows my preferred method of magnetizing bases, and it has some ideas on re-basing, which is relevant for anyone going from squares to rounds or vice versa.
For a reddish mars-desert looking effect for the necrons in particular you might also try GW's martian ironearth (cracks) or ironcrust (clumps) basing effect paints. I haven't used these, and I heard they can be a bit finnicky to work with, but the effects seem to be worth the hassle. Here's a couple videos about them:
Definitely test any new basing methods on some blank test bases first, but I think you'll find a little bit goes a long way to really helping your models come together.
