Well, if every Comapany will have multiple users, you shouldn't let every user to change its connection string. There should be an admin that would handle stuff for all the users of specific Company.

If every user in a Single Company will have a unique connection string then i'd say you didn't think this trugh and you should redesign your idea. Something is really wrong.

The same way as you do with any other data. ConnectionStrings are just Strings :)

Well i don't see that as a problem since Connection String is so small and your DB with them will be stored in a local DB. But then again i don't even see a problem of retrieving it the first time and storing it into users Session or even better cache it on Server side and you will have the access to it for all users from that Company.

Btw. may i ask why on earth would you want to have a remote DB for every Company??? Application will be much slower because of a remote DB and don't event let me start on security issues :)