There are several types of things that can be modded...I'll speak for the two that I am familiar with...
There are a bunch of text files that control things like ship stats, abilities (duration, antimatter cost, effects), technologies, etc etc...basically, most everything in the game that is not sound or graphics is likely controlled with simple text files...you won't of course be able to edit these files as they are since they are currently in "binary" format...you will need a program that converts these files from binary to text so that you can actually edit them (note that the game can read either, so you don't necessarily need to convert it back to binary, though binary is more efficient)...
All sound files are .OGG...if you have an MP3 file you can download an OGG converter online (there are some free ones out there) and convert whatever files you want to OGG...rename them and replace whatever sound file in the game you want to (which will likely be background music if you are just starting)...
I'm sorry I can't be more specific, there are just way too many things to try and describe...however, there are many guides written on just about everything in regards to modding...other people more familiar with those resources (MyFist0 and Harpo, just to name a few) will I'm sure soon reply to this thread with links...there are also tools that can be directly downloaded from this website...
Once you have a very basic idea of how to mod, I recommend searching for specific questions on google, these forums, or the resources others can provide you...if there is something you can't figure out, don't hesitate to post a thread asking a specific question...
In general, most people on these forums are very willing to help with specific questions that you have, but more general "blanket" questions like "How do you mod" are likely to get you responses with just links...its just that many of the pro-modders around here are fully aware of the resources available and (since they have hindsight) may wonder why you haven't gone there first...don't take it personally, it's not your fault you can't find something if you don't know it exists...hopefully some of them will provide you with links (I for one learned how to mod in an unorthodox way so I unfortunately don't know all those resources)...
Best of luck to you on your modding adventures 
