Probably this later idea is best.
100%. I would never want the water level over the top of the liner level, no matter how well you seal that connection, or how often. (Not to mention - that sounds like a repeat project that would quickly get annoying.) Imagine if you got water behind the liner... not a good scenario. And even the tiniest gap could allow several hundred gallons of water to escape. Maybe it would just soak in to the ground under the liner, but... maybe not. Next thing you know, you have a liner on top of the pond instead of under it!