Even with all the commentaries and interpretation aides out there, you may still come upon things when you read Scripture that appear to be at odds with writings elsewhere within it. A good rule of thumb to keep in mind is that Scripture, while a collection of separate books, is put together for a single purpose, so when you struggle to interpret the meaning of one thing, you must keep in mind that interpretation should not fly in the face of other teachings from the same collection of books. If you find such a case, it’s wise to assume your interpretation is probably faulty, not the text.
This is commonly seen in the New Testament books and epistles, where the teachings are aimed at different audiences. Obviously those audiences had different cultural backgrounds and held different beliefs, so you wouldn’t expect someone preaching the gospel to each group to emphasize the exact same thing. St. Paul talking to this group addresses different issues than St. James talking to that group. If you try to lump them all together as though they spoke to the same audience, one right after the other, it will definitely lead to confusion and, if unchecked, false ideas or doctrines.
It’s very prudent to use study aides, but really the only “safety net” is going to be your willingness to ensure those interpretations coalesce with the Church’s teachings. Asking about this up front is a good sign you’ll do just that.