Well, the answer is quite easy:
- if you work with unit processes, then you need to include elementary flows (this is what you mean by environmental flows, I think?) where they occur, so emissions in these processes where the emissions happen. If you look at some generic databases, you see how this is meant to be done (and can connect these processes to those created by you).
- if you work with system processes, they already contain the elementary flows from the "rolled up" supply chain, as overall calculation result, and you can and need to take them as they are, there are very rare cases where you can reasonably change them in system processes.
Hope this helps!