So I realized in Elder Scrolls Online when you reach level 50 you can go to other campaigns and everything will be revamped to your level, but one thing DOES bother me. Will we be able to keep and use wayshrines from our past alliances when we switch?
Yes, effectively nothing changes. You just unlock even more alliances.
Once you've beaten the main story of the game…
… Meridia thanks you and works with Sir Cadwell to…
… allow you to experience the other alliances in a "What if…?" scenario. E.g. what would have happened, if you'd be dropped off the coast of Skyrim rather than Khenarthi's Roost?
But that's just the loose story explanation. Technically you really just gain access to the very first wayshrines in the other alliances, allowing you to play that content (in a higher level version that is isolated from the players originally fighting for that alliance).
Note that this will be changed later this year with the introduction of One Tamriel. Details aren't known yet, but you won't get cut off of any content (except small instances related to story quests once you complete those).
The game is designed in a way that you can't miss content. If you miss picking up or reading a book in such an isolated story instance, you should be able to find copies of the same thing somewhere outside once the associated quest is completed.