The example you gave is a little confusing for the following reasons:
- "depends on the number"/ "(not) by the number" instead of "per number"
- Second sentence and first sentence say the same thing but contradict each other on what is true (rule vs policy). Remove one of the two sentences.
Do not use "and" if you start a sentence. Do not use a comma if that is the last statement you are concatenating.
Here is one example.
Our license depends on the number of processors and not on the number of users. Do you have any such offerings?
We prefer to license your software by the number of processors. Our policy does not allow to license by the number of users. Do you have any such offerings?
If you need to have more than one concatenated element in your sentence, you should group all the elements with "not". If the sentence becomes too long, it is always better to break it down into smaller sentences.
Our license depends on the number of processors, hard drives, memories and not on the number of users, managers, developers. Do you have any such offerings?
I have to add: it makes a difference if you have a second verb or not.
Notice that in the sentence you gave, there is only one verb:
Our license for the server depends on the number of processors and not on the number of users.
In this case, it makes more sense to use and because both share the same verb.
However, if you had a different sentence like this
Our license for the server is usually discounted by the number of processors - not that we cannot do the same by the number of users.
then it makes more sense to not use and in the above sentence as each element is dependent on a different verb.