Which is correct when writing emails?
- Everything is fine at our/your end.
- Everything is fine at our/your side.
Between those two sets of choices specifically, the first is correct.
However, using 'our side'/'your side' isn't the part that's wrong in the second examples, it's the preposition: you can be at an end, but you are on a side. So you could say "Everything is fine on our side."