It ca be in JCR or filesystem.
Thanks for letting me know, I current project that I am working in has a requirement to give the richness of ADAPTIVE Forms to the end user to submit the form, guess I have to create a Template and Theme in AEM 6.0 for a defined Schema and also develop the XDP for approvers to view the filled form by the end user with a less richness or use the XSD developed in Designer on AEM as well as Assign Task in livecycle with both having no big richness.
Also I have one more question, in case Assembler service is used to built a XDP with multiple input fragments, should the resultant Document be persisted in JCR to render the same as HTML 5 in AEM 6.0?
As of AEM 6.0 GA release, it is not possible to use any AEM Form that is stored in AEM repository, directly as asset to the Livecycle Assign Task Activity. In order to do that, either you have to copy the Asset in LiveCycle LCA as well or somehow write an intelligent code for example, which passes this PDF form to LiveCycle process as input while invoking the process which then can be further used in Assign Task as document variable.
By the way, if you were talking about Adaptive Form, those are not supported by LiveCycle workspace, currently.