Hi - as some of you know, I have a Cubase setup.
I have different types of projects:
First it's the idea projects where I just record in ideas and try to stick them into a folder structure of categories. After I had 2-300 ideas I found out it was smart to make .mp3's of all ideas so I can easily listen and put them together. Opening Cubase just takes too long.
Then there's the song projects, where I have more or less a finished concept. If it's not for an album, I have this in another folder structure of categories.
Then there's the album projects - here I create folder structures like "need lyrics", "to drums" - "with bass" and this changes as I work through the project.
When I work out stuff, I start out with roughly arranging stuff so I have a pretty much working mix with bass, keyboards and all. Often I just record a refrain and verse and copy it around, stretch the time and play with it to get it just right.
When done with that and lyrics, I start on recording phase. This time I had live drums, so I had to prepare the tracks for the drummer first. This meant recording some bass again and making sure nothing was out of beat for him.
Then it's nitty, gritty work getting the bass on first, move on to the keyboards and guitar that doesn't need my Marshall amp.
Then it is into studio getting grand piano, guitar solos and vocals on it. For this I need to mix it up again, so we don't waste time in the studio on that.
Finally get the backing vocals and all extra arrangement in at home and send it off to mixing and mastering (with a LOT of guidelines). I usually oversee both pretty closely but try not to be too much of a pain in the butt.
During this I will probably have played the same bass, keyboards and guitars 2 or 3 times ... it's a slow process, but it works for me.