I personally Love foobar. I love how small it is and how quickly it loads my library. I migrated from winamp to foobar about 5 years ago now, and haven't looked back. I just didn't like how bloated the software was getting. This was in the winamp 3.0 days.
I don't really change much for settings. I like the Album list + Properties (tabbed) layout the best as it gives me quick organized access to my music. To get the albums to show up go to file>preferences>media library> then hit add and point it toward your music folder. Takes a minute or two the first time you set it up but it will incrementally update the list every time you open the program.
Here is mine as I've got it.

I like to set up hot keys for volume up, volume down, next track, and pause/play. I primarily use a laptop so it's handy.
That can be set up through file>preferences>general>keyboard shortcuts>addnew
The only other thing I set up is the conversion stuff, as I need to compress flac files to vbr 0 for my mp3 player.
Right click on file in playlist>convert to>...
you can set the output file settings there as well as the naming scheme I use %artist% - %album% - %tracknumber% - %title% which comes out as Jackson Browne - Solo Acoustic Vol. 1 - 01 - Barricades of Heaven
Thats just preference though you can set that stuff how you like.
Flac is supported out of the box. Mp3 compression will require the lame.exe which can be easily found with a quick google search.
As I'm a function over form kind of guy I haven't messed with skins or other addons but I did find this tutorial which looks fairly thorough.
CODE
http://www.overclock.net/sound-cards-computer-audio/312177-foobar2000-guide-installation-skinning.html
If you have any more specific questions I'd be happy to help you out with those.