Is there a way to replace a clip in AE but, maintain my IN point. Seems to start at the beginning 

Yes — when you replace a layer's source (Option/Alt-drag onto the layer, or Layer > Replace Footage), the layer keeps its in/out points but the new footage always starts at its own beginning. That's expected behavior.

To make the replacement start at a specific point, select the layer and slip it with the Pan Behind tool (press Y), then drag left/right. This shifts which part of the source footage is shown without moving the in/out points. You can also drag the slip-edit bar that appears on the trimmed layer in the Timeline.

More details in the official docs: https://helpx.adobe.com/after-effects/desktop/work-with-layers/select-and-arrange-layers/selecting-arranging-layers.html