Any tips for aligning fenders?
I think the first step would be to work out what is causing them to fall out of alignment. Possibilities include:


Vibration when riding causing fitting screws to loosen or parts to rotate
Leaning your bike against something when parked
Someone leaning their bike against yours or tampering with them


In case 1, you can remove the screws and refit them with some threadlocker (a weak glue that keeps machine screws/nuts in place, usually blue in bike applications).

In cases 2 and 3, the stays may be getting bent or fastenings rotated, in which case all you can do it be careful how you park the bike and where you leave it.