There are a number of ways to learn which verbs to conjugate in compound tenses with être or avoir. 

Most (non-pronominal) verbs will always conjugate with avoir, there is a limited list that always use être, (see attached links) and a further limited list that conjugate with one or the other, depending on usage. Many of the latter are specifically in more advanced lessons, although some are fairly frequently used verbs, so you will encounter them along the way.

Pronominal verbs (reflexives and others) always conjugate in compound tenses with être (if you are not sure about these, search on this site and Laura Lawless site for starters). 

Yes, it takes time but it is not a matter of having to learn EVERY individual verb as you go - if you know the 'être verbs', you will know the far more numerous avoir verbs by exclusion !  

https://progress.lawlessfrench.com/learn/theme/9611820

https://www.lawlessfrench.com/grammar/auxiliary-verbs/