Yes, marking the secondary is a bit iffy. I'm worried about getting it clean again too. Marking the Primary does not matter as it's center is blocked by the secondary when using an eyepiece. So long as your original center spot is very close to the center, then a de-focused star at high magnification will show nice concentric rings. Only re-spot it if it is obviously out.
Marking opposite the focuser just aligns the focuser to the tube. As I said, my focuser needed 2mm on one side to straighten it up as it was 1/2inch off center when looking through the LightPipe at the secondary. Using the LightPipe you will see if the secondary is not centered in the focuser, so that should be close enough.
At f/6 and for visual use you can ignore offsetting the secondary. So OK to skip that.
But, measure that it is central to the tube and that the vanes are square to the tube so they block the minimal amount of light down the tube. The vanes are usually adjustable with thumbscrews???
Oops. I missed the bit where you said you used the 6mm too. that's probably a good choice for planets, but also as you have found longer eyepieces give nicer views and coupled with a barlow can give you high magnification with wider fields of view. Quite often longer eyepieces have wider fields of apparent view due to their design. I don't mind saying it confuses the heck out of me.
I have a 30mm in 2" and a 26mm in 1.25". You would think that on the face of it that they deliver almost the same view due to similar magnification. But no way! The 30mm in 2" has a very large apparent field of view.
Just found this -
http://jayandwanda.com/digiscope/vignette/afov.html
"AFOV is the field of view through a telescope eyepiece at it appears to the eye. AFOV is determined by multiplying the actual field of view by the scope's magnification. For instance, a scope yielding a 2 degree field of view at 20x magnification would have an AFOV of 40 degrees.
Most eyepiece makers supply AFOV information for their eyepieces. As a general rule, Plossl designs are usually limited to no more than a 50 degree AFOV. Also, at focal lengths much greater than about 30mm, the barrel of 1.25" eyepieces will tend to limit the AFOV to something less than 50 degrees. For instance, a 40mm eyepiece with a 1.25" mount is usually limited to around 44 degrees. Copyright © 2003 by Jay Turberville"
Mark.