thanks for your quick and helpful reply Kambiz. That has cleared a few things up for me.

I now think that what I want to achieve was the 'Transformation to mean head position' process outlined in section 4.5.2 on pg51 on the Maxfilter (2.2.10). The steps of which are are: 

1. Process the file using 'Head position estimation' 
2. Load the result file containing the quaternion channels and select 'Movement correction task'.
3. Then load the file containing the mean transformation as the reference head position

So I think I first need to create the quat.fif through the -headpos 

maxfilter -f run1.fif -o run1_quat.fif -headpos

Then movement correct the quat.fif and transform using the mean head position (mean_trans.fif)

maxfilter -f run1_quat.fif -o run1_quat_tsss_mc.fif -st -movecomp -trans run1_mean_trans.fif

I obtained 'run1_mean_trans.fif' from run1_quat.fif using the 'save mean head transformation' in the maxfilter gui
	(Is it possible to run this step from the command line? Kambiz - I see you asked this question here in Oct 2012 - did you get a solution?)

Can someone please confirm if running these commands will apply  tsss to run1.fif and transform the data to the mean head position of run1? 

If so then will the commands below apply tsss to run2 and transform the data to the mean head position of run2?

maxfilter -f run2.fif -o run2_quat.fif -headpos
maxfilter -f run2_quat.fif -o run2_quat_tsss_mc.fif -st -movecomp -trans run1_mean_trans.fif

I'm unclear where (if at all) to apply the '-frame head' and '-origin fit' commands fit into to these steps. So if someone could comment on that it would be very much appreciated.

cheers
Craig