Only one official map does lifts, if I remember correctly (Hightower).
I'll have to doublecheck the vmf (You should as well), the payload still continues as normal upwards, but the cart keeps it's original orientation. (An option in the path_track properties) Now, the part I don't remember correctly is how the lift works.
There's two ways that I remember it working, but I know only one works:
1) It's an additional tracktrain that moves forward when the cart moves forward, and moves back when the cart rolls back.
2) It's a dynamic entity that gets parented to the cart when the cart reaches the path_track at the bottom, so then it can move up and down with the cart without the need for double the path_tracks.
I have a feeling it's neither, but the whole question of syncing it up and what not is not hard to do if you double-check everything.
Now then, I have 2 questions for you:
1) Is this for a Payload RACE map or just a Payload map? I.E. Pipeline or Badwater? Because if it's like Badwater or Goldrush, you're gonna have to deal with the auto-rollback that occurs with the cart. Using the above methods will work in Payload Race, but only the first will work nicely in a single cart map because constantly parenting and unparenting objects is gonna crash something at some point.
2) About your question of how it'll work in the beginning of a map... Not sure if it's a smart idea, unless designed very well. Any sort of uphill section with rollback is designed as a chokepoint, and a lift straight up or any sort of up should be considered as such. So, you're basically starting your map off with a chokepoint. Unless it's meant to be super-difficult for a team (ala Gorge), something's not gonna work.
All the above assumes you know what I'm talking about and that I read your question correctly. And if you're just starting with the tools... may God help you in your quest, cause you're gonna need his help. Or Boojum. Either one works.