Yeah, crypts are a fair bit more troublesome without a map. With automap, you just mark every one you happen by when doing anything else, easily returning when needed. Without... you basically have to delve it as you find it, otherwise leave it to maybe be re-discovered. Also, it helps to leave an indication that you've finished a crypt, such as a campfire.

I hate those cheapo crypts. :P Especially when they're loaded with baddies! "I shouldn't have bothered..." Then sometimes you get the barely-guarded bonanza.