I'm going to be GMing a new Deathwatch game soon, my first time GMing in nearly a decade. The game is going to be online using Skype and maptools. My question is; how do you guys handle maps for the actual combat? Obviously the FFG books have virtually nothing in them by way of maps, leaving it all open, and I've been searching around the internet for something that's going to be of sufficient scale but with very little luck.

First suggestion: use Roll20 instead of MapTools. I do the same as you actually: all the actual IC and OOC talk goes in Skype, for the superior logging, rolling and maps are all on Roll20. Best advantage over MapTools: Roll20 is browser-based and doesn't have a person acting as the server. Makes things run much more smoothly imo.

I generally create a couple maps in the day or so before a game, players understand if I have to pause a few minutes to gen a new map.

Ideally I would not use maps at all though. I play a lot of games where we abstract positioning and distance, it saves the GM a lot of time, he just has to make sure to accurately describe the scene in a way players can understand it without a map. Unfortunately FFG40k's heavy crunch doesn't support this very well. I wind up making my map scale too big sometimes, because making it small overwhelmingly makes it too easy for the players, in my experience.

I do PbP and normally in the DnD and Pathfinder games on there the GM uses photoshop to draw really simple maps on an easy to read grid.

I am more comfortable with pen and pencil so I bought graph paper and drew my maps. I usually have 1 square on the paper represent 2 meters.

In combat I lay out positions and obstacles from a bird's-eye-view and then the players give me their round actions. They are represented as different color dots with the first initial of their PC name representing them. Enemies are usually always red.

If I use pen, I use whiteout to represent former positions to not confuse current positions. I draw hash lines to represent movement and in parenthesis put the round that they performed that movement.

If you are creative you can at least come up with SOMETHING to give them for reference. Again, like Ksha said, imagination is a great tool by itself.

Roll20 has great map tools for GM's