I merged two datasets in plink1.9. It worked, but I did get the error "multiple positions seen for variant" and "variants have the same position". How do I resolve this when trying to merge the datasets again?

Since you are using Plink to merge two datasets, I would exclude the variants with multiple positions from both the datasets before merging.

For the second part of your question, did you also try merge_eigenstrat of admixr package?

https://bodkan.net/admixr/reference/merge_eigenstrat.html