A bit of background on this, as it shortens the essay down a lot. Jira Service Desk is an application which adds and modifies functions over the top of a standard (core) Jira project.
So it can be helpful to thinking in layers. Jira is a layer that provides issues, fields and agents. JSD is a layer on top of that providing more.
Your agents get to see both layers and are expected to work mostly in Jira. Your customers only get the JSD layer (so the portal, email and knowledge base). Configuring a JSD portal is actually a lot more about getting the two layers to map their functions together than it is about configuring a portal (for example, Jira has a workflow but your customers only really care about parts of it, so one mapping is "what we show customers when status is x". Another is mapping request types to issue types - your customers don't care if their request for X is a bug, feature, change, thingy, but if you map the request to the right issue type, you can make it look easy for them while still classifying and handling the issues efficiently)
Custom fields are a Jira thing, not a JSD one, and hence the same "mapping" applies.
You can create lots of custom fields for your issues. Then, you can put them to the customers by using the project settings -> request types -> fields.
I think you have got 95% of the way there - you've added fields, they're working on the issues, but you are not yet asking the customers for them. I think you just need to tell the request types that they should be asking the customers for your fields.
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