I think in order to make it display properly, you have to use English Bible verse system. It has to be exactly the same.
The problem occurs when the User Bible has different verse numbering system.
Accordance also has problem with its own Bibles when the parallel Bible has different numbering system.
I have pointed out a related problem here.
What I would do is to change the User Bible verse numbering to exact the same as the English Bible. You may have to separate a verse in your user Bible or group two verses together, depending the difference between the User Bible and the English Bible.
Here are some examples:
The English Bible does not have 1 Chr 21:31. The Chinese Union Version has it. 1 Chr 21:31 in CUV is exact the same as 1 Chr 22:1. Therefore, I changed the verse number of 1 Chr 21:31 into 1 Chr 22:1 in the CUV. Then I make comments in the parenthesis.
Screenshot 2014-12-08 17.27.59.png 234.88KB
The CUS does not have John 7:53, but the English Bible has. Therefore I created John 7:53 in the CUS, and made a comment in the parenthesis that the CUS does not have this verse, and the its content is included in John 8:1 in the original version of CUS.
Screenshot 2014-12-08 17.28.30.png 103.05KB
The advantage of User Bible is that you can manipulate the content when necessary.
The major problem is that when the original text has different numbering system from the English Bible.
It is not a user Bible problem, but a problem in Accordance itself. This is the problem I pointed out in the post I mentioned above.
An indirect way is to tie the English/User Bible with the original text, rather than making parallel text. Then the problem of Rev 12.18 in my post will be solved. However, you also lose the powerful feature of the tagged text in the parallel window.