Most headunit remote outputs can supply up to 500mA. Most amps use somewhere in the order of 150mA (hence the 3 amps max per headunit rule). If you only have one amp and your fans will use less than 350mA combined (will depend on the fan), you should just about be ok.
2 of these would be 360mA:
http://www.coolercases.co.uk/details/fan_xinruilian_18a.htm
Whereas 2 of these would be 800mA - a big no-no:
http://www.coolercases.co.uk/details/fan_xinruilian_40a.htm
To be extra sure, just check how much current your amp draws on the remote lead (assuming that info is available).
Don't forget that if you blow your headunit's remote output by drawing too much current, they're expensive to fix/replace, and then you'll probably have to resort to a wired power switch for your h/u, or forking out to fix it.
If you want to do it *right* though, you should really hook up a relay on to the remote output from the h/u, so that you can draw much higher current.
HTH
Mark
