Hi, this is rather a vague question, http://musicbrainz.org and http://acoustid.org are both open websites with lots of information but in summary musicbrainz recordings ids are given to a unique recording. Acoustid are given to a fingerprint of actual audio, in an ideal world there would be a one-one correspondence between the two but in reality neither database is perfect, nor able to model all real world cases so this isn’t the case.
You don’t really have to make a decision about just consider the preferences available within Jaikoz and then run Correct Metadata from Musicbrainz to fix most things. Use the other tools in Jaikoz such as Match to Specified Release and Manual Match to Musicbrainz to fix the cases where Jaikoz doesn’t do such a good job.
Also Jaikoz can also Match to the Dicogs database that contains many releases not within MusicBrainz, however it doesn’t have a concept of Acoustids and can only be used to match whole album not individual tracks.