So I have clamav the antivirus but is that a protection against rootkits or do I need to install rootkit hunter as well with clamav?
Clamav only acts as an anti-virus, and does not protect you against rootkits. In the opinion of most people viruses are not such a big threat on Linux, however we can all agree that rootkits are so it is good to protect yourself against them.
rkhunter will need to be installed on a fresh install before any software or updates are installed because it looks at changes in the system, and assumes the system it is installed on is safe, and then compares that to the system's state later on when you do a scan.
So if you have a rootkit already, and you install rkhunter, it won't be able to tell if you have one or not.
Another option is OSSEC HIDS (Host Intrusion Detection System - which is not required to be installed on a fresh install, and will be able to detect a rootkit on a system even if it is installed after the rootkit (in most cases)) which can detect rootkits as well as a larger range of system activities.