The short answer to your main question is you�ll pay in Jan 08 and July 08 for tax in the year 06/07. Now you�re self employed HMRC may also sting you for advanced tax for a tax year not yet complete, but let�s not worry about that now�..
As this is the first year you�ve registered to be SE, I expect that they will send you a paper return unless you�ve registered for online tax returns, in which case they�ll send you a letter to remind you to do it. If you haven�t had any of these so far I recommend you register for online services (it takes a day or two to set up, so don�t leave it until September). This means you�ll get an instant calculation. Whichever method you choose, you�ll fill in one return with pages relating to self-employment as well as the normal bit. It�s all pretty straightforward.
I�ve just done mine as a SE for the 3rd year, always with a PAYE bit too.
Hope this helps.
(PS � this isn�t a silly question. You should see some we get��..)