I used to approach it differently but nowadays how I'd do it is probably as follows:
Over time, save up some ideas you feel have potential, even if it's just a melody, progression, etc.
Sit down and rework those progressions, melodies etc. in as few sessions as possible so they have more of a general cohesiveness. Add or remove tracks where necessary to fit your idea or concept.
Once you have a really rough layout of your album, and your progressions, melodies, etc. laid out, give yourself some time to figure out how you want to execute each track, then start at track 1 and move your way forward through the album track by track, creating a more developed "skeleton" of the album.
This method may seem a bit rigid but I think if you're working with a concept/theme it's a good way to keep things in line and make sure you're not being redundant or confusing in your message.
So now that you have a rough version of all the tracks, this is when you lock yourself in your studio for the next month or two and flesh them all out. I feel it's really important to work on this part of the process as consistently as possible, so that your full talent and potential at that time is put into all the tracks equally. Doing it this way will also ensure a consistent sound quality between tracks.
I know there's many ways to "skin the cat", this is just the method that I think works best if you're really shooting for a theme or concept album. I know this is how some of the greatest concept albums were made and it makes a lot of sense to me..