depends on the question which application you mean. The WLS Console and the FMW Enterprise Manager will be using the same port since it will run only on your admin server. BI specific applications running on both instances (like bi server, bi presentation server,...) need own ports. So what you did was totally correct.
However, I went ahead with the approach of changing the Weblogic port as well.
Theoretically speaking, re-using 7001 for both the instances should work, since the EM / Console allows you to choose a particular domain.
However, i was a little unsure about the manner in which the same 'weblogic' user could be reused for both the instances. This is because you are asked to setup a new password for weblogic when creating a second domain. So was confused as to how one user could have 2 different passwords to log into the same 7001 EM/Console.
Due to this, i went ahead and used 7031 for the second instance. I now have two weblogic users, and access two different EM/Consoles, one for each instance.