Thanks Doug,
I have all relevant files and am aware of both SOFs; I'm sure my original problem explanation was confusing. I have the entire project directory accessible to my machine (including both SOF files, the PTF, etc). The problem is that they aren't 'registered' with the SOPC builder, and as such cannot be found by the maze of bash and perl scripts called via the Eclipse plugins. I can successfuly create, build, and flash my code via the command-line, and so generally my problem is solved. The lingering question is how to code/flash against a project built somewhere else, e.g. without the project 'Registered' through Quartus/SOPC; that is, how to do this without hacking perl scripts or wading through command line options?
Sincerely and thanks again,
Ryan