it's pretty much getting used to it, like with the pad. The stick works in the same way in that you're really pushing two inputs, but there is a square restrictor (if it's a standard sanwa stick), so there is a certain spot to feel for. However, riding the gate isn't optimal for a person using a stick, because of the longer distance it takes to go the whole way, so any person planning on getting the most they can get out of it will just memorize the motion for diagonals without going all the way to the edge.
The one hard thing to do with a square restrictor is to not hit diagonals. Because left, right, up, and down do not have their own spot to click per se, since they are in the middle of the edge, and not on a corner. A lot of people like to replace the square with an octagonal gate so every direction has its own edge, but I personally like the square after getting used to it.
Everyone makes mistakes, and just because you use a stick, it doesn't mean you won't ever slip up. Granted, a game like soul calibur you don't have that many things to screw up because of the relative ease of execution, but in many 2d fighters, even experienced people on sticks still mess up quite a lot, so execution will always be an issue that never disappears.
If SC is the only fighting game you'll ever play, I think with the right amount of practice, you can get to the level of comfort you want on a pad even, I'm assuming you've only been playing for a few months, and it takes most people longer than that to get as good with a stick as they were with a pad. However, if you are planning on playing 2d fighters (you should, they're more fun) then a stick is definitely a good investment, because the limitations of a pad have a much greater impact (face buttons, range of motion on your thumb, and how agile your thumb is compared to your wrist).