.MTS files are using a highly compressive codec called H.264 (an MPEG-4 codec) to store the video in a relatively small file.
iMovie transcodes those highly compressed videos into another format (.mov) using another codec (Apple Intermediate Codec) for better editing.
As H.264 is a Long-GOP (GOP = Group Of Pictures) format, it does not store every frame, but interpolates between keyframes (the content between keyframes is calculated while playback).
The Apple Intermediate Codec is an editing codec, thus every frame is stored in the .mov file, thus smoother playback us guaranteed.
If you don't want to edit your footage, it is just best, to copy the complete content of the SD card to your folder of choice and preserve the file structure (make one folder for every card to copy into).
As you already deleted the source files, and obviously just want to store the video and not edit it, you can use the
iMovie > Share > Export Movie(CMD+E) command to make a highly compressive file out of your .mov files. There are plenty of guides available to guide you through this.
But you can also use
MPEG Streamclip to transcode the .mov files to .mp4 or .mov files using the H.264 codec. If you have several video files, you can use MPEG Streamclip's
Batch List:
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Maybe have a look at Advanced Search to find dozens of similar threads about MTS files and Mac OS X an editing them and storing them and so forth:
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