So i will probably end up with a persistance system between scene.
That is a completely different problem. You can have a large level if you prefer, that could work if your levels arent that big, but you'll need to manage memory somehow. You either fit everything in memory or stream parts in.
That said, its a completely different, pretty hard problem that isn't really anything to do with tk2d - you will need to figure out how to handle a large streaming world + persistence in Unity first - usually with additive levels and managing persistence somehow without losing performance. Or you could make levels and have load screens, etc.