NEVER transcode from the cards. The card (entire structure and every file) should always be copied to a hard drive. These are your DIgital Tape. Then you can transcode with Mpeg StreamClip, Compressor or Log and Transfer in FCP (MB Grinder is a for cost program that has some nice features)
The files off out of the camera have no TC so there is nothing to reference the edit to transcoded media later on. Do yourself a favor, Log and Transfer and edit, This can be done over night or a long break, then edit. Everything will be faster from that point on. (Search about editing H264 in FCP)
Using Log and Transfer adds Timecode to the video also.