I have 33 points in physics SE. Not much but enough to make upvotes. I recently had a question on chemistry SE. What I found that Points don't add up between the two sites so I can't upvote. But as I know the two websites are linked. In what way are they linked and how.
The sites are on the same network of sites -- the Stack Exchange network. Your accounts are linked network-wide as well; when you create a new account on another site using the same credentials; it gets added to your network account.
However, reputation doesn't add up. The communities on each site are separate, and so are the reputation values. Reputation is tied to the privilege system, which includes community moderation tools. Someone who knows the policies on closing question on Physics may not know the policies on Chemistry1.
Note that once you get 200 reputation on any site, you get a +100 bonus on all sites you have an account on. In addition to that, if you join another site, you will start with 101 reputation (thus bypassing most new user restrictions -- you'll be able to upvote and comment).
Also, as a Chemistry moderator, welcome to Chemistry.SE! :)
1. That being said, in this case the two sites follow almost identical policies. But that won't apply for a pair of random network sites.
The purpose of reputation on Stack Exchange sites is mostly to codify the degree to which each site trusts each user. because the detailed rules differ from site to site rep is not transitive or transferable.
However, because the most basic features of the engine are the same from site to site, users that pass a basic threshold (200 rep) on one site can associate accounts to get a small bonus (100 rep) on all sites that will allow basic actions.