You may want to have a look at using "forced overflow". For release 11.3, it is documented in the Documaker Server System Reference manual. With forced overflow, you can define "X" number of overflow records to print on form A and the rest of the overflow records to print on form B. Form A would be the back of the invoice, defined to use tray 1, and form B woud be defined to use the regular non-perf paper tray.
Hope this helps,
The first printable section on the page determines certain attributes about your layout including the tray and duplex selections. It is important to note that "printable" does not necessarily mean there is anything on the section that actually prints. Therefore, you could have two dummy/placeholder sections at the top of your form - with no size or content. Specify them as headers and copy on overflow. Have the first one specify tray 1 and the second tray 2 (your trays may vary) along with the other page attributes that are important. You will need to specify recipients and triggers (if needed) for the sections - just like any section that you expect to print.
Once pagination occurs those two headers will copy on overflow to the newly paginated pages.
Use a PostTransDAL rule in your AFGJOB that runs a script that essentially does the following.
while( HaveImage( "MyTray1Section\3", "MyForm") )
Of course, you want to use your actual names for the tray controlling section and the form that contains it. Since you know that your form is duplex and that you only need 2 occurrences of the section, the \3 designated on your section name means to find the 3rd occurrence of the section on the named form. You keep checking and deleting the 3rd occurrence until there are no more. At that point, your first sheet will have the necessary tray defined, but all succeeding sheets will now have what was your "second" tray controlling section now in charge and will print on a different tray.
(It may be important to note that the \3 does not mean "third page" it means 3rd occurrence. Technically, you can have multiple occurrences of the same section on a single page and this is how you would reference them separately. That is why you don't change the \3 occurrence between deletes. Although technically you are referencing the same section name, you are always looking for the 3rd occurrence to delete. Once they are gone, then only your first sheet will have the necessary section at the top.)