Well I don't know specifically about EKM but have migrated a sitewizard store to nop and also a custom e-commerce solution to nop and you have a number of options here. My advice would be to avoid SQL unless your products are quite flat. Writing all the mappings for images, categorys attributes and so on is going to take a lot of effort. Not saying impossible though.
Your best option would be to use the nop API perhaps with a command line program to bring in your exported data I have done this a few times and generally this works best for me YMMV of course.
You do have the Excel import function, but I think that may only work if your product structure is simple enough to map everything - you might be able to get away with taking an excel output from EKM and converting this into the spreadsheet format that the excel import in nop requires.
You also have to think about product images for example can you get them out of EKM easily and with a filename you can match to when you import back into to nop. Depends on how accommodating your existing provider is too - wen I did the export from sitewizard the feeds were so bad I ended up using the Google Analytics feed to get what I needed.
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