If a command seems stuck, it can also help just hitting the Esc key a couple of times.

CC3+ should handle negative numbers just fine, just make sure there isn't an extra space between the minus sign and the number.

Also keep in mind that you have two options when typing coordinates.

Either you type the destination coordinates outright (112,45 or 112,-45 etc.), and in that case you don't use negative numbers since all the coordinates in the map are positive (except some special templates)

Or, you use the relative coordinates for a relative movement from the move origin, in which case you prefix with @ and negative numbers means downwards and leftwards (ex @10,20 or @-10,20 or @-10,-20 etc.)

You can use the TRACED command to trace it automatically, but you do need to make a small config file change to work around a bug in the current version.

If you have entities that are completely identical (same position, same properties), you have to select them by entity tag number (scroll down a bit on that page to find the specifics for that particular one).

And yes, the group tags you see in the list output is also an entity tag number, so you can delete a whole group that way. (Individual entities inside a group can only be selected if groups are unlocked, and the group tags can only be selected if groups are locked).

Last's years annual may be of interest as a starting point. It contained two issues dedicated to graveyards and crypts.

This is a dungeon style though, but if you are going to a zoom level where you can actually see such details, you kind of end up there. For larger scales, city, and especially overland, such details tend to disappear.

As far as I know, there aren't any necropolis styles for overland or city, but perhaps some of the darker styles may be appropriate to provide the right mood, like Darklands and Darklands City.