The engine we use is (unfortunately) not too user-friendly to edit, because all of the file formats had to be figured out by the fans... so there's a lot of different tools that are only suited to very specific tasks, and there's still a lot of unknown variables around (meaning there are things we still can't edit, like the AI behavior for example).
Mission programming is done entirely by scripting in WCPPas (there is no graphical mission editor advanced enough to make proper missions), but the scripting language is fairly easy to learn and definitely allows for very complex missions.
Importing 2D bitmap graphics into the game will require you to use one of about 3 or 4 different tools, depending on what features the bitmap has or what function it will have in the game (ship texture, menu element, background image, etc)... some of these tools are command line tools, but they're all simple to use. The downside is just the time you will waste due to lack of an "all-in-one" image conversion tool.
To convert a ship into the game's format you need to go through a bunch of different tools (and depending on which 3D modeling package you used to make the originals, you might have to convert it to another format before converting it to the game's format) which are probably the most complex of all WCP modding tools. Making changes to previously converted ships half of the time means re-doing most of the conversion process...
Most of the tools we use were made by Mario "HCl" Brito, Thomas Bruckner, and our mission programmer PopsiclePete - you can check their personal websites (from the CIC's Links page) for documentation on each aspect of editing the game, and if you still have any questions you're welcome to ask around the Fan Projects section of the forums, most of the team usually checks that forum as well... but if you're looking for an easy-ish way to put your gaming ideas to practice, or if you're new to modding "barely documented" engines, it will really take you some time to get the hang of this one.
