Okay, your question is straight-forward, but has a complex answer...
First, to just answer your question: You may consider the knee braces to be effective supports for DEFLECTION and calculate deflections based on the span between the connection points of the knee braces. This presumes your knee braces are relatively short compared to the span of your rafter/beam.
Next, for strength you should strongly consider jike's recommendation of a computer model, however working it out long hand is fine as well, but your structure is automatically indeterminate and not necessarily easy to work out. Consider the brace as pin-connected to make your job easier; Also it is near-impossible to make rigid connections for this situation in any material other than steel (not counting rare materials like Alluminium, where I really don't know). Pay close attention to the shear introduced into the knee region above the brace in the column and behind the brace (towards the knee) in the rafter/beam.
Finally when designing the brace be sure to give due consideration to the way in which it will connect and any eccentricity inherant due to the brace shape. By this I mean you need to consider the secondary effects of a non-symmetrical brace member like a sigle angle.
DO NOT use eccentric connections. There are lots of papers and procedures around for eccentric connections, however most are based on flawed research out of the US. Unfortunately the research was quite competently carried out, well written with the best of intensions and just happens to be wrong for most out-of-the-lab applications. Because it was well written, seemed perfectly reasonable and greatly simplified the connection it has been widely reproduced. That doesn't make it right, or undo the structural collapses (yes, plural) which have occured due to the use of the detail.... You can design an eccentric connection, but it is NOT easy and should come out VERY inefficient. If the numbers don't drop like a rock, your design method is likely based on the incorrect procedure.
Good luck,
YS
B.Eng (Carleton)
Working in New Zealand, thinking of my snow covered home...