Howdie mate
Someone actually worried with the game design is refreshing.
Most FPSC users are more level designers that build while they think instead of putting time and effort in thinking, studying and prototyping.
In my opinion (and each game designer as it's own), the process is:
1. Concept
Write down your main idea, sketch the story, the pros and the cons you think your game will have. Give it a rest for a couple of days then read your notes, rethink it. When you have a solid idea, proceed to the next step.
2. Design Document
Get your hands in a nice design doc template or write your own. Some people write a small design document with the overall about technology, gameplay, level design and storyline. In the FPSC context, it's basically level design and storyline since the engine is picked, the genre also.
There are extremely indepth design documents, which are very useful in case there are programmers that only code with no game design interferance (sp?). Some say a "perfect" design document will leave no room for doubts for programmers and artists.
3. Gather media
Self-explanatory... gather the media
4. Prototype and build
Start puting the storyline and level design up with the engine. Again, with FPSC this process is easier.
5. Test
Self-explanatory also.
6. Review
See what you are missing, check your goals, go back to Prototype and Build (only building probably at this point)
One day, you break the loop and your game is done.
This is my opinion, for the real juice, try this:
http://www.gamedev.net/reference/
About half way down the page you will find a section about game design and another about level design. Those should help you out. There's a great template for design document there also. I think it's called ctaylordesign.doc (something like) but it's way too indepth for a FPSC doc, although you can get the piceture with this.
Good luck and welcome to the amazing and frustrating world of game design.
I'm pretty sure I know everything. Doubts are something rare in me and I am never wrong, as this signature can prove.