Tim,
The arrows should line up so the heads are pointing at each other. They are indications of were the wedge in the the elements cancel each other and the biconvex element is the crown and faces the sky.
You should have between 5 to 10 thousands clearance around the diameter of the elements vs the ID of the cell. If the cell is too tight it will pinch the optics when it cools and it also cause one to easily chip the edges trying to get it in and out the cell.
Does the metal lip on the inside of the cell have three raised areas at 120 ° apart ? If so, these areas should be aligned with the foil spacer between the lens elements so that you get even pressure when the retail ring is applied.
The lens should have a slight rattle when you place it in the cell and give it a light shake. Check it in two direction that 90° apart. Either the elements or the cell might not be perfectly round. My friend's 6" Schupmann had a cell that was out of round and was pinching the optics. The lens rattled just fine in one direction but was very tight in the other. Opening up the cell made a huge difference in the images.

- Dave