It is fairly common to see isle used where aisle would be appropriate, but the different meanings are straightforward to grasp.
- a passage between rows of seats or seating areas
- a passage between rows of cabinets and shelves (containing goods)
- a lower part in a church parallel to but divided from (by pillars) the nave or chancel
- an island
The similarity between isle and island is a useful indicator of which word to use. If the thing you are writing about is not an island, you know that you need to use aisle.