Of course it it important to put your ware axis perpendicular to the wheel when your trim it. More precisely, the pot axis should coinside with the axis of wheel rotation if your goal is to trim straight and even.
So if the wheel is not leveled, the pot axis should be out of level to the same degree. However, since we don't have any easy way to measure and adjust the angle, the simplest approach, indeed, would be to use such a common and inexpensive tool as a bullseye (cleverly suggested by Marcia) and have both, the wheel and the pot bottom, leveled.
But, again, when you throw a pot (incl. use of needle tool, etc.), its axis will coinside with the wheel axis of rotation automatically regardless of the position of the wheel head in space.
So, for simple symmetric forms, the goal is really to return the pot you're going to trim to the same position relative to the wheel in which it was when you created it.
Similarly, if you even out the top of the pot with your needle tool, that top will always be parallel to the wheel head, since the rotation of the wheel determines the plane of the cut.
This is only true if you hold the needle tool at the same exact angle of your wheelhead being off.
Neil is right. You hold a needle at a particular spot in the space at a certain distance from the wheel head. When the wheel head rotates, it moves your pot, and the needle cuts it at the same distance from the wheel head all around. So the rim plane of the pot will be parallel to its bottom and to the wheel head.
Naturally, it will be true only if your pot axis is perpendicular to the wheel head. And it will be even if the wheel head is not leveled. Simply because when you open or close the cylinder, your hand is also fixed in space as the above mentioned needle tool. So every portion of the cylinder wall that comes in contact with your hand will be forced to move to the same position relative to the wheel.