Yeah, it can be a little weird getting used to a stick for the first time. I remember constantly ending up with accidental tiger knees when I was trying to do low tiger shots with Sagat years ago *laughs* . If you have a way to see your inputs displayed, spend some time using that and just practicing doing basic motions (qcf, dp, dashing, hcb~f, etc.), trying to do them without any extra inputs. Remember to practice the motions facing both ways, too! I know that sounds obvious, but a LOT of people overlook it and then cry that they can't dash to the left or something. It's alright to "ride the gate" (push the stick as far as it can go) at first, but you'll want to eventually be able to do motions with as little movement as possible.
As far as gates, it's pretty much personal preference. I like square the most since it gives you precise diagonals (good for command normals like Kyo's d/f+D) and it has less maximum movement than octagonal, plus most arcades with japanese setups that I've been to are square gates, as well as most japanese sticks (if can you ever need to borrow someone else's).