In theory, a Moleculo-type library with Illumina sequencing could distinguish the two repeats. In practice, many users have had limited success with this approach.
Personally, I would recommend PacBio sequencing for an unambiguous answer. There are also a host of new (e.g., optical mapping) and old (Southern blotting) techniques better suited to your task than short-read sequencing.
The assembly will merge it into one. Then, when you align the reads back to the assembled genome, that region will have twice as much coverage. You can use one of many CNV analysis tools to detect that.
See this paper for a CNV analysis overview: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4394692/