My approach is to store things as normal on my PC, and then use Allways Sync (or similar tools) to replicate those directories to my local DropBox, and then allow DropBox to do it's magic.
I treat the files in their original locations as masters and only do one way replication via Allways Sync to DropBox, so if ever I *were* to change something in DropBox the change would not propagate back to my PC.
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