You just need to set the image size before you 
scan.   Rubberslug wants you to keep them at 
360 pixles wide, not sure what that is in 
inches but the software will let you chose units 
of measure.   For standard cels that is about 
45% ish of the original size.  They'll let you go 
up to 560 pixles wide for oversize cels.   While 
your at it you should set your output resolution 
no higher than 100 dpi for faster loading.  
Does this help? or are you more confused?