Best way to handle that is to make sure the layer the grid is on is frozen. That's usually the HEX/SQUARE GRID layer.

• Yes. Anything you do in-map (using allowed resources) is perfectly fine. The main thing here is that you cannot find your own symbols/fills from outside the allowed resources, because this causes distribution problems for the atlas.
• Yes, that is fine.
• Yes. I usually prefer to have these on different maps, because CC3+ can really only maintain one scale in any given map file, but there are cases when things work best together.
• Nothing against tokens directly (as long as they adhere to the allowed resources), but generally having monster tokens on the map makes the image export a bit weird, anyone downloading just the png file from the atlas would have a image file with immovable tokens.

If it is just things getting to dark in the shadows, maybe consider just lowering the opacity of the Wall Shadow effect instead of trying to add point lights?

The point light system is a completely different way of creating shadows, and doesn't work with the well shadow effect. Which means that if you want to use it, you can't just set up a light source in the dark corner, you have to properly set up lighting for the entire room.

Am I understanding you right here that each sheet is one floor, so that all the floors are in the same map file?

In CC3+, because of things like sheets effects and such, maps tends to use a lot of sheets, so it is generally better to use one map per floor. Although it is possible to keep it as one map too, but then the macros hiding the sheets must be updated to hide the complete set of sheets. With some nice naming you can do this rather easily by taking advantage of the HIDESHTF and SHOWSHTF commands which hides and show sheets by a wildcard filter, so for example all sheets for floor 1 could be named FLOOR1_SOMETHING and so on.

If you're looking for something in particular, the atlas is fully searchable, although there are no search option for interesting locations though.

To pick a spot, find some feature on any map that looks like it could hold a dungeon. Could be a cave, or a ruin, or a building (both on the overland map or a city map)), or perhaps there are some stairs or holes in another dungeon out there that may lead to yours?

And note that the mega-dungeon always could use new levels. It is already a crazy place with levels completely different from each other, making it a good place for anyone just wanting to make a dungeon level without looking for a specific location in the atlas (Just remember that mega-dungeon levels should have exactly one entrance from above and one exit going down so they can be linked in a long chain.)