your idea is very good, and I did this before too.
PNG supports transparence and so you can export parts of your picture.
If BlackInk could Import a second .png into another layer would be great, to do all the work in this application.
But you can export two different parts, rework them and in the end merge them with some gafik tool like "gimp" for example
btw. they will add layer featurs in the next steps:
-Collapse layers together
-Layer transformation tools / Load in image into a layer
Black Ink upcoming features Link:viewtopic.php?f=29&t=49