I'm assuming you're wanting to setup a lighttpd server on a different physical server, so you'd probably just want something reallly simple (no cpanel or anything) and then just install lighttpd & an ftp server yourself, that way there would be minimal load on the server. Also specs probably wouldn't need to be very high, since there wouldn't need to be much processing going on.
Or if you were wanting to set it up on the same physical server it'd have to run on a different port, say 8080, and could be installed side by side with apache, just a little more configuration needed. Although with that solution you probably wouldn't see that much of a performance advantage, and some filtering services may block servers running on ports other than 80 (I know my school used to, college does).