It would be a whole lot easier to show you how to do this if we had the SKP file which you could attach.
I would take care of the off-axis thing first. You should be able to rotate it the required angle to get it to align with the axes. You might find turning on hidden geometry will help you with that. A guideline parallel to the axis closest to the axis on which the cylinder is aligned could be useful, too. If the cylinder is a component or group and it is rotated inside its bounding box, open it for editing and rotate just the geometry.
Once you have the cylinder aligned, close the component or make it one. Then the Move tool will make it simple to rotate the cylinder to the standing position. Hover over the component/group and look for the red crosses. Move the cursor until it shows a protractor over one of the crosses on the side. Click and rotate the component/group into the vertical position.
Placing the plate will be easiest if it is a component. You can move the component's axes so its origin is centered on the bottom of the plate. The origin will be the insertion point for the plate. Put a couple of crossing guidelines at the bottom of the cylinder such that they intersect at the center. Import the plate into the cylinder model and drop it at the intersection of the guidelines. After you have the first plate in place you can make a stack of them by using the copy function of Move to make a linear array.
