Assume you are reading two academic papers every day. What strategies can I use to decrease the possibility of confusion between the two?
I do of course not know what your current work strategy looks like so I can only provide what I think are generally helpful tools.
Note-taking should be a priority, not only to avoid confusion but also to help you get an overview. set a target to summarize the paper in a about a page and try to capture the following:
What is the major question covered by the paper?
Why is it important?
What was done (experiments observations data)?
What are the major conclusions of the paper?
Did you find any new information of particular interest to you?
You may come up with similar or different key questions depending on th epurpose of your reading. The point is to make such short summaries of the papers.
Once you have the summaries you could consider organizing them in some fashion. There is no exclusive model to use and in fact the organization may depend on the purpose of your reading. You may find that after reading a number of papers a possible way to organize them can become clear. The main purpose of this step is to bundle papers that have specific points in common.
You should also sort your papers (printouts or files) with your notes. There are many ways of doing this rom the analogue to data bases. Try to use a free reference data base system to get everything organized.
As JeffE has suggested, some confusion with reading papers is both expected and desirable - I can always tell which paper's I've read closely, versus skimmed for a little bit of information, because they've got scribbles in the margins.
And therein lies my recommendation: Thoroughly, carefully interact with each paper. You're not just "reading" them in the same way one reads a good novel. Annotate. Take notes. Find places where the author seems to have taken a leap and make sure you agree with them. If they don't show the steps for something, see if you can puzzle them out for yourself. If you don't understand a bit of math, etc. work it out until you do.
It may also help to read from two related but distinct fields, so that your papers don't feel "the same". For example, one empirical and one theoretical paper. Or a wide scale review and a single study.