The way it's going to be released digitally, according to: http://www.newsarama.com/comics/hank-kanalz-batman-beyond-unlimited-111116.html, is that on the first week of a month they will release Chapter 1 of Justice League Beyond and on week two they'll release the second chapter . On week three is the first chapter of Batman Beyond and the second on the fourth week. The print collection of all of these would be released as Batman Beyond Unlimited in week three, including the Batman Beyond second chapter that would come to digital the following week. Each digital chapter is $0.99 and the print collection is $3.99 so it works out to the same price in the end.
One way to go about it obviously is to just add it as Batman Beyond Unlimited and list Justice League Beyond as some sort of back-up. However since Justice League Beyond is released prior to the collection there would be the two dead weeks where someone would want to post and would be unable to, unless the issue page was created early and the person was allowed to edit for just the JLB (Justice League Beyond) part.
My proposition is that Batman Beyond and Justice League Beyond gain separate volume listings. Then at the top of the page is a note that it is collected in print form in Batman Beyond Unlimited, which would also have its own page. That way as new chapters were added digitally they could have their own issues and if people want to review immediately they are able.
Also, in the wording of the announcement of the series (http://dcu.blog.dccomics.com/2011/11/14/dc-comics-launches-batman-beyond-unlimited/) they said it would be collected "from various digital first series". This suggests more than just these two series will be inhabiting the "Beyond" brand. Possibly there will be a continuation of the Superman story from August, or something like that. With multiple series being produced at the same time, they could only release one of them in the pages of BBU (Batman Beyond Unlimited) so having separate pages for each series would allow for them to all to be covered.