Why would someone not do autopartitioning if it's so much easier to do?
Are there any concerns about log files overflowing your hd if you do autopartition? By that, I mean, if you had a separate partition for logs, then if it overflowed, it would just mess up the logs not your whole system. Sorry if that didn't make sense.

I guess I am asking why wouldn't someone choose autopartitioning?

Auto-partitioning is all very well - but it's useful to be able to control what goes where. For example, if you have an existing OS on the hard disk that you want to keep, or you want to have dedicated disks or partitions for things like /home, /usr etc.

I can't see any obvious problems with having a separate partition for log files; however, log files aren't all stored in the same place. A lot are stored in /var/log, but there are a lot that aren't too. Having a separate partition isn't the solution - what you need to do is to get logrotate configured to rotate and remove log files appropriately, and for syslogd to only log pertinent information.