You can list multiple subclips for each clip, and it's really quite simple and intuitive to choose which to import, add, remove, all under the Logging tab. Subclip'd clips will show a IN/OUT overlay on their thumbnail, and you can globally clear subclips by selecting all clips, right-clicking, and choosing Clear Subclips from the contextual menu. The Transfer software keeps track of how many subclips you create on a clip...if you make Subclip 1, and then later delete it, the next subclip from that master clip will be named Subclip 2, regardless of whether or not the first subclip still exists. This behavior is retained when the software is closed and restarted. And it makes sense...that way you can never have a conflict with subclip names if you go back and pull in more clips. On transfer, subclips will have an additional number sequence designating they are a subclip. If the master scene clip was named 700_0007_01.mov, subclips one and two would be 700_0007_01_01.mov and 700_0007_01_02.mov, respectively. FYI, clip number designations are derived from a setting in the Others menu of the EX1...you can set the number sequence and reset the clip count as you wish.
To transfer clips from the SxS media, simply select the clips you wish to import, ensure the "Send to Final Cut Pro project" option is ticked, and hit Import. Now is a good time to grab a cup of hot joe...transferring a full 8GB card over USB seems to take around 10 minutes. I'm told that ExpressCard slots are much faster (one user quoted "5min or less for a 16GB SxS card"). As the clips are changed from raw MP4 streams into MXF MOVs, they begin appearing, as if by magic, in the Final Cut Pro Project window. Each clip in the transfer window will indicate if it is being transferred or in queue, and a card clip countdown is shown next to the card name in the left sidebar. When the transfer completes you can kill the XDCAM Transfer software and start editing. The transferred clips are stored in folders matching the card name within the XDCAM Import Location (which is set on the first time you run the software and configurable within the Preferences). Organizational nazis will probably want to change this setting on a project by project basis.
On the subject of organization, here's a few notes on metadata that is transferred. If you manually add a clip or subclip Title in the Transfer software, that is carried over to FCP in the form of the clip's actual filename in lieu of the numbered name. Manually marking a clip or subclip as Good OK in the Transfer software will tick the Good option in FCP's Item Properties > Logging tab. Likewise, the Transfer software's clip/subclip Comment field maps to FCP's Log Note. Transfer software's Creator field doesn't appear to map to anything in FCP. In the import method I outline in the paragraph below this one, the Comment and Good metadata does not get automatically transferred into Final Cut. So if you are manually adding metadata to clips in the XDCAM Transfer software, use the "official" method outlined above.
That is one way to do it...perhaps the official way. Let me tell you how I made the process more streamlined for me, and why. Whether you initiate the XDCAM Import from the File menu or by right-clicking in your project window, the imported files will always show up in the root of your project. You can try the import from within a bin, but no dice. The bin is ignored and the files go to the main project root. Specifically setting a bin as the Logging Bin has no effect on where the XDCAM Transfer software imports clips. In every situation they end up in the root of the project window. For a project organizational freak this is most distressing. You quickly end up with a project window littered with unhelpful clip names like 400_0007_01. Then you gotta make bins, drag all the files into those bins, pray to $DEITY that you didn't accidentally select and move a sequence or other file into the wrong bin, etc. Very messy and most irritating. Here's what I did. Instead of initiating the import from within FCP, I would mount the camera/card and load up the XDCAM Transfer software myself (it's in your Applications directory). It acts, walks and talks the same way with the exception of a missing "Send to Final Cut Pro project" option. But no worry. Next, I select the Untitled card on the left sidebar and name it in the info tab. These names have to be fairly short (probably a FAT32 thing), the software will warn you if it's too long. Then I just hit CMD+A to select all the clips on the card, and hit Import. The clips are massaged and transferred to a folder with the new name you chose, in the XDCAM Transfer Import folder (which is set when you first start the software, or under the Preferences for Import Location). If you don't first name the card, you'll end up with a jumble of files in a Untitled folder. After the transfer completes, I right-click in my FCP project window, select Import Folder, and browse to the appropriate folder name under the XDCAM Import directory structure. Bam. A new bin with a name that makes sense, chock-full of the files you just transferred. This process takes little or no extra time than initiating the transfer from FCP, and the end result is that I control the bins the clips get imported into. Much cleaner overall in my opinion.