I'd just braid the entire area where it's sticking up to be safe, and be sure to braid the "unruly" bits with the "ruly" hair..that's what I did with my horse (same problem, big cowlick right in the middle) and now it lays flat.
The longer you keep it braided the better, but it's good to change the braids pretty regularly (just take them out during grooming/riding/working/etc and rebraid before putting him back), about once a week..and keep with that pattern for maybe about a month or so. Also when you braid the hair, it should be at least damp, and braided pretty tightly (but of course not so tight that it will be uncomfortable to your horse)
Also if you want to you could invest in some MTG..the stuff REALLY works. Following the instructions on the bottle I saw a visible change within a week. I tried it on a cut on my horse's hock and it had considerable stubble growing back on it by the next day, I was very impressed!
Good luck =)
Last edited by rocky pony; 01-17-2010 at 07:38 PM.