I own a 1990 civic dx... recently its had an engine replacement (1998 civic dx)... my problrm is the altinator belt...
I blew onne the other day and while replacing it noticed the groves on the engine pully aren't the same as on the altinator... the engine has a 3 slot and the alt. only a 2... the belt I bought for the 1998 is a 3 slot so it fits the engine but sits slightly off on the alt.. . its running smooth right now with no issues but should I replace it with a 2 slot belt ? Or is my best solution to replace the alt.

You should replace the alternator pulley with one that matches the rest of the system, it should be possible to swap the pulleys instead of the entire alternator.

Ditto.

It may run fine now but it could break or slip off at any time and also by the belt not having proper grip on the alternator pulley you could cause the belt to prematurely wear