Say I want to search all my library for the word "love" but I want to exclude all my Greek books or all my Hebrew books? I have all my resources tagged "Greek" "Hebrew" etc. but I don't see any way to exclude a given collection from a search.
Create a new collection that excludes your other collections (you can drag collections into the "minus these resources" box). To create collection of all your resources, use the rule rating:>=0.
An alternative would be rating:>=0 -mytag:greek -mytag:hebrew or whatever your tags were.
There's more on collections here: http://wiki.logos.com/Collections
Do collections differ from tagging?
Yes. Collections can be built from things like tags, author, subject, publisher, resource type, etc.
You can very quickly create two collections:
This can take about 60 seconds to create once you know how.