The error and access logs are stored in ~/.logs/apache. They are separated by machine and domain. Your ~/.logs/apache directory is updated once every 20 minutes from the "real" logs in /var/log/apache2 on the machine that serves your virtual host. This is almost certainly navajos.
It is expected that you don't have permission to read your logs in /var/log/apache2. Instead, use the handy domtool-tail program to view the logs in realtime. For instance, this command line will dump the last entries in the access log for www.domain.com, in the style of the UNIX tail program. We assume that you have Domtool permissions on domain.com.
domtool-tail [-n LINES] www.domain.com access
The optional -n LINES argument will fetch that many lines from the log.
You can view a graphical representation of your access logs by browsing our webalizer interface at https://members.hcoop.net/webalizer/. Its statistics are updated once per day.