You can use Automator Apps and iCal. Just create two Automator workflows, one to open Transmission and one to close it, then set up repeating events in iCal and set the Alarm function to "Open file". For your 1AM event, choose the Automator App that starts Transmission, and the other for the 6AM event.
cron would be more efficient, but you would have to know a bit of Terminal commands. Basically you'd create a file called "crontab" and in it place a line that reads something like this:
15 6 * * * open [path to file or application]
The numbers at the beginning are a sort of reverse time code, in this order:
Minute Hour Day Month Day of the Week
So if you wanted an Automator App called "StartTransmission.app" in your Documents folder to start at 1AM every day of every week of every month, you'd do:
00 1 * * * open ~/Documents/StartTransmission.app
For the second script:
00 6 * * * open ~/Documents/StopTransmission.app
Those can be in the same file, on separate lines. Save it as crontab, as plain text without any file extension (don't just hide it) then go to the Terminal and enter:
crontab [path to crontab file]
That will tell the computer to run those tasks in that crontab file at the specified timeframe.
EDIT: LOL, see you're already familiar with cron, after I typed out that long post. Oh well, the first way's still easier although I still think cron would be better.
jW
