You could set up custom logs in your httpd-vhosts.conf depending on the HTTP_HOST variable – if your server is an Apache and you use subdomains for each single site.
For sub directories:
SetEnvIf Request_URI ^sitename1 sitename1
SetEnvIf Request_URI ^sitename2 sitename2
CustomLog sitename1.log common env=sitename1
CustomLog sitename1.log common env=sitename2
not tested