Does it matter which way the cables run to change to 2 6v golf batteries... for my xantrex inverter?
Not quite sure what you mean by this. If you had two 12v batteries (and I'm assuming that you mean your xantrex inverter is 12v), then those batteries were in parallel. Therefore, you had a pair of "bridge" cables connecting the batteries, one between the two positive posts and one bridging the two negative posts. Then you had a negative cable from the interter to the negative post on one battery and a positive cable to the positive post of the other battery.
When you're going to two 6v batteries, you'll need for them to be in series. You'll want a link cable linking the negative post of one battery to the positive post of the other. That will leave you with two bare posts, one negative and one positive. Attach the negative cable from the inverter to the bare negative post and the positive cable to the inverter to the bare positive post.
So, yes, it does matter which way the cables run. But basically, if you have a negative cable from the inverter and a positive cable from the inverter they will be attached to a negative and positive position on the batteries in both cases. The difference is that the 6v pair will be linked in series and the 12v pair will be parallel. (If, BTW, your inverter is 24v, you'll need 4 6v batteries, all in series. What voltage is your inverter?)