You can certainly apply rules based on sending or recieving domain, and have completely separate rules inside of them. Most of the features on the system to be applied based on sending or recieving domain or email address, and of course, global.
What specifically are you looking for with separate logs? As the system currently exists, all mail processing logs are written to one file. It is quite easy to sort out individual messages from the log, but it is not possible to record to different log files for different messages.