I can't decide whether to keep the help desk application in the same database as the rest of the corporate applications or completely separate it.
The help desk application can log support request from a phone call, email, website.
We can get questions sent to us from registered customers and non-registered customers.
The only reason to keep the help desk application in the same database is so that we can share the user base. But then again we can have the user create a new account for support or sync the user accounts with the help desk application.
If we separate the help desk application, our database backup will be smaller. Or we can just keep the help desk application in the same database, which makes development/integration a lot easier overall, having only one database to backup. (Maybe larger but still one database with everything.)
What to do?
I think this is a subjective answer, but I would keep the help desk system as a separate entity, unless there is a good business reason to use the same user base.
This is mostly based on what I've seen in professional helpdesk call logging/ticket software, but I do have another compelling reason - security - logic is as follows:
Generally, a helpdesk ticketing system generally needs less sensitive information than other business system (accounting, shopping, CRM, etc). Your technicians will likely need to know how to contact a customer, but probably won't need to store full addresses, birth dates, etc. All of the following is based on an assumption - that your existing customer data contains sensitive or personally identifiable data that would not be needed by your ticketing system.
Principle 1: Reducing the attack surface area by limiting the stored data. Generally, I subscribe to the principle that you should ONLY collect the data you absolutely need. Having less sensitive information available means less that an attacker can steal.
Principle 2: Reducing the surface area by minimizing avenues of attack into existing sensitive data. Assuming you already have a large user base, and assuming that you're already storing potentially useful data about your customers, adding another application with hooks into that data is just adding further avenues of attack into the existing customer base. This leads me to...
Principle 3: Least privilege. The user you set up for the helpdesk software database should have access ONLY to the data absolutely needed by your helpdesk analysts. Accomplishing this is easier if you design your database with a specific set of needs in mind. It's a lot more difficult from a maintenance standpoint to have to set up views and stored procedures over sensitive data in order to only allow access to the non-sensitive data than it is to have a database designed to have only the data that you need.
Of course, I may be over-thinking it. And there are other compelling reasons for going either route. I'm just trying to give you something to think about.