Betsey - i'm not trying to tell you how to run your Exchange environment, but ...
ideally you should have your Exchange transaction logs writing to a different place than the actual stores (really, not just to different folders or logical drives, but to different physical spindles - i know, not always possible in all places).
You should never manually clear the log files - if you're running out of disk space, you need to get that infrastructure fixed. When you manually clear the transaction logs, you make any sort of recovery difficult.
You must use the BE Agent for Exchange.
The BE Agent for Exchange should take care of the log files for you. You do not select the folder from the server tree - when you are using the agent, you select the information store.
Now, when BE (and the agent) finish the information stores successfully, the agent then sends a signal to Exchange to flush the transaction logs. So, this is your "point in time" clean database for a recovery. Then, exchange starts writing a fresh set of transaction logs.
When it's working correctly, you can see all this interaction very clearly by stepping through the entries in the event log on the exchange server.
Cheers