I'm assuming you basically want to stop people from hammering your server? i.e. limiting the number of requests any person can make.
Many sites stream the downloads directly via PHP scripts, since PHP scripts are singled threaded so its impossible for the users download manager to start downloading in multiple chunks
You would then link to this file, something like
http://yourDomain.com/download.php?filename=xxx.zip and it would send the xxx.zip file.
WARNING - be very careful doing this though, do a lot of sanitizing on the filename value, be sure to strip slashes, only allow predefined files to be downloaded.
NOTE - Its VERY important that you do not send any other output, only data read from the file should be echo'd out,
I've not fully tested this code - personally I use something a little more simplistic -
Alternatively you could take measures directly via Apache -
http://www.webhostgear.com/279.html
I Hope this helps.