If I remember correctly, you have to first register as an employer, with the section that deals with PAYE/CIS.
Then once you recieve your UTR number, registering with the CIS people is prety straight forward, and can be done over the phone.
Then when you employ a Subbie, you phone the CIS help line to verify the Subbie's status, and they will tell you how much Tax to deduct 0%, 20% or 30%.
Then monthly from the start of the tax year, you have to fill out I believe it's called a CIS300, detailing how much you have paid out, to whom and how much tax you have deducted. You have about 10 or 11 days to return this form otherwise you will be fined £100. You have to fill it out and return it even if you don't employ anyone, for as long as you're registered.
If you fill it out On Line, they will stop sending out the forms, so you will have to remember each month to go On Line and submit it.
Then every three months, you will have to send the deductions to the PAYE/CIS department that you first registered with.
Again, if you are late, you can be fined £100. They are not as bad as the CIS for this, the CIS will send out the fine automatically, and every month they don't receive it another £100 fine. Of course, you can't fine them if they fail to send out the form.