Full primary drive mac pro. what next?

I have just about filled my primary drive so purchased additional 1TB drives for the second and third bay as I understand I have to keep my primary drive less than 100% full to maintain efficiency.
The question is how and what do I transfer off the primary drive to the second bay and how do I do it?
On the about this mac dialogue box it just lists the drive as full with "other". Are there any preferential items to move off the primary drive. I already reference my aperture library to an external hard drive.
Is there a simple way of doing this?
Thanks a million.

I have not had an issue... going back to 10.2 which was really just beta OS X.
YMMV but it is simple to do now. People do it different? or they don't leave the /Users on the boot drive, or some screwed up program that doesn't follow the rules (never run into one myself).
Every application also lets you change where in preferences.
Some want to use symbolic links.
Dedicated boot drive works for most anyone. I used 15K SCSI, then 10K Raptors and WD VR as well as SSDs for boot drive. Home is often raid, some go with mirror, some stripe or just one drive.
There are as many different setup configurations as people.
Cost / Performance SSD $1.50 per GB while 10K VR $0.50 and the difference in MacPro is now very close and allows you to have a faster boot drive - I have tried and always found the WD Black in the past to not keep up with either of those. But they have gotten better but so has everything.
Even now 1TB Black goes for $125 for 1TB (last summer they went for $80).
The only rule is backups and bootable clone and know how so you can restore and manage.

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