The 5-domain limit on the Site Owner and Site Owner Plus licenses is applied to all existing top-level domains on the server. Unfortunately, there is no way for you to define which domains will be counted towards the limit.
You can either remove unused domains or, if you require more top-level domains than five, you can upgrade your license.
It is not possible to assign some domains to LiteSpeed and the rest to another server (e.g. Apache). You cannot run LiteSpeed together with another server at the same time.