Hi jbells, welcome.
The way you make queries is not always the "inverse process" of how the index is built, you'll grasp that concept with a bit of practice, so creating a query from the annotated model would rarely cover a real world use case, it's way more likely that for a specific query you need to select a subset of fields, and apply some options to the way they are used.
See
the first query example in the reference documentation, it uses a MultiFieldQueryParser which is handy to implement what you're asking.
So you need to define a set of fields to be considered, but no more work is needed. The boost factors defined as entities are applied at index time, so there's no need to specify them again at query time (that will get you a different result).
In more advanced chapters there are some hints about when you should consider index-time boosting or query time-boosting; it's very advanced (read: hard to maintain and understand, rarely used) to define boosting at both query time and index time, so especially during your first experiments avoid it unless you're an expert in scoring, relevancy and precision of information retrieval systems.
Let me know if this is more clear to you now, or we might consider improving that first chapter.