Finding the Best Practices for long alter table queries

Sure, you could use percona tool for alter table.

you could find reference as below link.
https://medium.com/@soomiq/altering-large-mysql-table-using-percona-toolkit-on-aws-aurora-acb6e57a33d4

But I recommend that you could use gh-ost for that. it is trigger-less which I think much better than percona online schema change tool. I have tested and it works fine with aurora 5.6 & 5.7

https://github.com/github/gh-ost

Hope this could solve your problem.