do you "plant" your front leg a little? Ie where ever the ball is bowled does your front foot end up in the same place?
In terms of judging line, it helps if you know where your offstump is. if you see here...
http://custombats.co.uk/cbforum/index.php?topic=5322.msg76526#new I have gone into a bit of overkill about taking guard and where you stand!
Without seeing you bat, it is difficult to help more other than to suggest that your head/eyes lead where your foot should go, rather than the old "get your foot to the pitch of the ball" which describes what the shot looks like, rather than how you get into position.
To explain what I mean about getting your eyes over the ball and you feet will follow, see if you can find on youtube a clip of Ian Bell batting well - when he is in, his technique, especially through mid on is fantastic, which seems to be your issue.