Problems importing footage with Canon GL-2

I'm brand new to Mac & FCP, migrating from Casablanca after 8+ years.
I've had no luck using the "Capture Batch" option, so I've reverted to "Capture Now"...after reading lots of issues with the gl2. "Capture Now", though very time consuming, seems to work okay. I'll need to break the clips for editing. I'm thinking wedding recepiton (with lots of rec/pause). Using "Mark" then "DV Start/Stop Detect" works nicely, but when I trim the clips and put them in the timeline with a transition (such as page peel), the clip somehow continues past the end. For example, as the page is peeling back, the same piece of video is under the page...then it cuts to the next piece of footage, and continues the peel. FYI, all transitions do the same. I'm just using it as an example.
However, if I trim the pieces of video and put them in the timeline instead of using the above proceedure, the transitions work perfectly. BUT, unless I use the method above, I'll have to scrub through hours of footage. The Casablanca has an "auto split" option. I dump the footage, hit the button, and end up with a bunch of perfectly cut clips. FCP has to have something similar...
Thanks in advance for your input
Stan

Use Log & Transfer with USB.
Make sure in the Settings that plain stereo is selected.
Al

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