I just did two nested rides including a SS1000 nested in a BB1500 as you specifically mention.
I used the instacert process as outlined here.
https://www.ironbutt.com/premierapp/instacert.pdf
using the link through the store.
https://riders.ibaestore.com/premier/pages/submitRide.cfm
I used one submission for both the main/top level ride and the nested ride, do not submit the nested ride separately.
I did so based on these instructions.
When applying for a nested certification within a longer event you must tell the verification team specifically that you are claiming the shorter event. In the cover letter for the cert package put in a remark that clearly states your request. For example; "During this 50cc Quest coast to coast challenge I rode the first 1,500+ miles in under 24 hours and claim Bun Burner Gold credit. I have included the added fee for certification of the BBG along with my 50cc fee."
I added my note just as above and when I payed my fee I added the $20 fee for the nested ride to the amount for the main ride certification fee.
You will need to provide a separate Spotwalla trip link for each ride. One single link for the main cert is not acceptable as your finish point for the nested SS1000 is different.