I use a 360 controller and yeah the analog stick with the official drivers is a pain, so i use the unofficial XBCD 0.2.7 driver which allows you to remap the 360 controller so for FF7 i don't need Xpadder or any program like that (so you can just change the d-pad into the analog stick and also change things like the back triggers into normal buttons and change the dead zone on the analog sticks to make them less sensitive).
Also if the arrows and number-pad isn't the directions have you checked in-game by going into CONFIG from the in-game menu then going to CONTROLS then set to CUSTOMIZE and at the bottom you should "up,down,left,right" and try changing those if the above isn't helpful.