Should I delete all my .MTS files? Help with workflow desperately needed

I use a Sony NEX 6 to film a lot of personal projects. My workflow has so far been
Film Import to lightroom Export as H.264 to hardrive Import to iMovie
But now I am going to start using final cut pro x. Apparently Final Cut X is unable to import .MTS files so again, workflow at the moment is
Film Import to lightroom Export as H.264 Import to Final Cut Pro X and convert to ProRes
My hardrive has quickly filled up and I've realised that I stupidly have my footage saved in 3 different locations. Lightrooms catalogue (.MTS), the file on my hardrive that I export the footage from lightroom to (export as H.264 but file type says it's mp4?) and Final Cut Pro's catalogue (ProRes).
I want a system where my footage is saved in one place on my laptops hardrive, then I will back my computer up with an external hardrive.
How does this workflow sound?
Film Import to lightroom Export as H.264 Import to Final Cut Pro X Delete footage from lightroom Delete exported file on computer Backup laptop on external hardrive
Can anyone suggest a better workflow?
Will I come across any problems in the future by deleting everything except the ProRes files?
Is lightroom a good enough program to be exporting my footage from or should I use a dedicated converter?

Thank you for your help, yes I will be backing up elsewhere. I'm a massive noob at all this and after an afternoon of searching I think I've got my head around it.  Best option for future footage
Import AVCHD directly from camera into Final Cut Pro. Convert it to ProRes if I have the space or if I'm not happy with the speed of working with native footage. 
For all the footage that I have in lightroom but no longer have on a memory card my plan is to 
Rewrap the files (I'm using a trial of clipwrap which changes the .MTS to .MOV). 
Import the .Mov files into FCP, transfer file into FCP catalogue
Delete the movies from lightroom and the lightroom catalogue

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