MOV is a container format. "H264" or "ProRes HQ" are codecs that define the compression, color and other attributes of the file within that container.
Roughly comparable to still image formats: JPEG is a "container" format (image format) and for instance sRGB is a color space the image is coded in.
I'm not sure that's a fair analogy. JPEG is the coding format, analogous to H.264, MP4, etc. Sometimes you don't need containers. Apple, to protect their interests, insist on wrapping every codec into its MOV container, but this MOV container cannot be opened by QT on computers on which FCP isn't installed. A TIFF, DPX or JPEG image sequence has no container, but Apple can find a way to put all these images into a MOV, just so they can feel better. AVI is another container. Color space is a totally different concept to encoding. It's a whole different ball game.
However, MOV is only a 'container', and it does not change the coding in the footage in any way, while it is being ingested into the system. 'Transcoding' is changing the coding from one format to another - usually a total rewrite of the data. This almost always, in the practical world, means losing data in one way or another. On a typical workflow, one tries to avoid transcoding as much as possible. Converting to Prores is transcoding, albeit to a format that can withstand heavy manipulation (like visual effects, color correction, etc). The AVCHD format is not robust enough to withstand heavy manipulation.
To a novice, I recommend using FCP if you have to be mac-based, or switch to Sony Vegas Pro for the PC.
Does your footage need heavy color grading or visual effects? Then you need to transcode to a more robust format like Prores (which has three flavors I think), or Cineform (on a PC), or an uncompressed file (like an image sequence). If not, you don't need to transcode at all. Edit natively (an i5, 8GB and two 7200rpm drives is all you need) and render on final output.