I do the same thing. I have one razor (a De Pews) that has a warped blade (i.e. bent) and also when I first got it an uneven bevel. The magic marker (we call them a 'Texta' here) allowed me to see the uneven bevel really easily and also decide on how to tackle the warped blade.
To hone this razor now (I have the uneven bevel fixed) I do three strokes on one side to every one stroke on the other. My reasoning for this is that as one side does lay flat on the hone all of the side makes contact for the full length of the stroke. However, the other side needs a rocking motion, as it doesn't lay flat.
As I use the rocking motion, the whole length of the blade doesn't make contact for all the length of the stroke on the hone; hence the 3:1 ratio.