If i have two panelboards nippled together and fed from the same 300a cb (main lug with feedthrough lug)would this be considered one panel.I have my branch cicuits all coming in one tub and some circuits passing straight through one tub to the other.Does it make a difference if the circuits are numbered 1-86(one panel 1-42 the other 44-86)

It's up to you.

Panel X - A 1-42

Panel X - B 1-42

OR

Panel X 1-84


Personally I like 1-84 or 1-126.