Don't you have both CS3 AND CS4 installed on your machine? I'm pretty darned sure you can have both; they're not mutually exclusive, to my knowledge. You do, however, have to install them in order: first CS3, then CS4.
I purchased CS4 Design Premium as an upgrade. I had CS3 Production Premium installed and then bought the CS4 Design premium upgrade.
Gotcha. Well, as I recall, you got application installation options in CS3. Failing a more authoritative answer than that, what's the worst that could happen if you tried installing AE alone? You'd have to install all of CS3, then install the CS4 upgrade to get back to Square One.
It could be worse.