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When mounting a video camera on a pole on the stern do you line the shot up on dry land prior to launch?
You have to line it up at some point... on land seems like a good idea.
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Do you spin around once on the water and carefully not move it as you turn it on?
Yep!
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Is the camera just running the whole time and if so...
Do you carry a fresh spare camera battery and empty SD card?
If you wanna catch the hookup, then yep, and yep! And then you go through 5 hours of boring footage to find the 1 minute fish fight and edit the rest out.
The VIO POV is a relatively expensive camera that allows you to kind of do your editing on the fly. Basically, when you catch a fish, you tell it to keep the last x minutes and it does. It'll overwrite anything you don't tell it to keep, so you don't run out of storage space as fast. But you'll probably limit out on battery time anyway.
The GoPro comes with a battery backpack that'll double your battery time. But that will only get you 4 - 6 hours at most.
If you shoot in low-def, you'll get more out of both battery and storage.
HTH.