You can create a user with custom fields via the API by passing in user_fields[1] like this:
curl -i -sS -X POST "http://localhost:3000/users" \
-H "Content-Type: multipart/form-data;" \
-H "Api-Key: d19b5a38ed13745f4c5..." \
-H "Api-Username: system" \
-F "name=cbbc7188c201b59ebc06" \
-F "username=cbbc7188c201b59ebc06" \
-F "email=cbbc7188c201b59ebc06@example.com" \
-F "password=b6629ed30b4bc3de32ce452d171540b0" \
-F "active=true" \
-F "approved=true" \
-F "user_fields[1]=a874d830b60" \
-F "user_fields[2]=732418b131b"
And you can update them by sending a PUT request to /u/<username>.json
