Yes, they are separate.  When you drain the master cylinder reservoir down, due to the open lines on the rear wheel cylinders, you may inadvertently introduce air into the front circuit feed line.  This would then necessitate bleeding the fronts, too.
  If it were me, I'd use this occasion to flush out all the old fluid (front and rear), especially if it's been 2 years (or more!) since the last brake fluid change.

YMMV,

Mike B.
  ----- Original Message ----- 
  From: Troy 
  To: vanagon@GERRY.VANAGON.COM 
  Sent: Friday, May 22, 2009 6:24 PM
  Subject: a quick question about bleeding brakes

  I have an 89 Westy. Are the front and rear brakes on separate circuits so that I only need to bleed the rears after replacing some wheel cylinders? It's not a major deal to do the fronts as well, but if I don't need to I just as soon not mess with it.

  Thanks,

  Troy