Try starting iPhoto holding down shift-option (if it's iPhoto 4), or opt-cmd if it's iPhoto 5 or 6. If it's 5-6, you may get a dialog asking you what you want to do, and one of the options may be locating your database. If you get that option, just navigate to it. If not, then do the rebuild option.
And without scolding, let me tell you that this is a lesson in Apple mentality. DO NOT try to outsmart any Apple application whose function it is to organize some aspect of your life (i.e. iCal, AdBk, or any iLife app). Don't move the files around. Don't futz with them. Let the app do its job and you'll love it. If you have OCD, just make yourself not look in folders like ~/pictures or ~/music so that it won't bother you. Every week there are a dozen threads complaining about things like this. I went through this when I got a Mac too. It works SO much better if you just close your eyes and let these things work the way the app designers want them to, and focus on more important things like taking photos and enjoying music. If you just let the application do its job, you and it will both be happy... or else of course switch to Windows!