How it differs from an essay
An essay argues mainly from reasoning over a limited set of materials. A research paper builds a position out of an existing body of evidence, and the survey of that evidence is part of the work rather than preparation for it. That changes three things: you need more sources, you need to show how they relate to each other, and you need to be explicit about how you selected them.
The research question
Everything downstream depends on this. A good question is narrow enough to answer within your word count, open enough to have more than one plausible answer, and grounded in something you have actually read. Questions invented before the reading tend to be either unanswerable or already settled.
Structure
Conventions vary by discipline, and your assignment brief overrides anything here. The common shape runs: introduction and question, review of existing work, method or approach, findings or analysis, discussion, conclusion. In humanities papers the middle sections often merge into a thematically organised argument, which is fine as long as the reader can still tell what is established knowledge and what is your reasoning.
Organising sources
Group by idea before you write. Build a simple matrix: rows for sources, columns for the questions you care about. What does each one claim, on what evidence, and where does it conflict with the others. The columns become your sections. This takes an afternoon and saves the week you would otherwise spend restructuring.
Presenting evidence
Report evidence at the level of precision it actually has. If a study found a small effect in one sample, say so. Overstating a finding is a more serious problem than a clumsy sentence, because a marker can see immediately that you either did not read carefully or chose not to.
Contradictory evidence belongs in the paper. Addressing it directly is stronger than hoping nobody noticed, and it is usually where the interesting argument is.
Discussion
The discussion is where you are allowed to reason beyond what the evidence strictly shows, as long as you mark it. Distinguish clearly between what you found, what you think it means, and what would need to be true for that interpretation to hold. That distinction is most of what separates a strong research paper from a competent one.