When customers log in to their account on our site we clearly know who they are and indeed have a Customer ID for them. SalesForces recognises this ID.
I would like to be able to have an application form available within this logged in area so that customers already logged in can fill in the form and the information in the form can be uploaded directly to their Account/Contact recrod in Salesforce.
Does anyone have any ideas about how we could pre-populate a hidden Customer ID field in the form?
In order to prefill a field, you can simply append it to the form address url. Here's our docs on this: http://www3.formassembly.com/blog/support-documentation/managing-your-forms/how-to-prefill-your-forms/ and http://www3.formassembly.com/blog/support-documentation/connectors-documentation/salesforce-documentation/how-to-populate-a-form-with-salesforce-data/
But what you describe is a bit closer to another technique ... our technique for setting up a Self-Service User portal in Salesforce: http://www3.formassembly.com/blog/support-documentation/connectors-documentation/salesforce-documentation/self-service-contact-or-anything-updating-in-salesforce/
The basic idea is that you create prefilled links ( see above ) using the server side code for your system. I'm not sure from what you're describing if your referring to a Salesforce User Portal ( or even general APEX ) system, or a home brew one. If Salesforce, the method in "Self Service Contact or Anything" should work. If a homebrew, let us know which one and I may be able to guess some more details for you.