Are you planning on doing a Transfer to Cloudflare Registrar?
Is your domain currently using Cloudflares nameservers?
By “setting” do you mean all the DNS records? Some will be detected automatically, but it is far more reliable to export all the existing records into a Bind format text file, and then import that into your Cloudflare account, and then manually verify that each record is correct. Once you have verified all the records you can start to change Nameservers. Personally, I would set all the records to be before changing nameservers, so nothing else should change during the name server change process.
What do you mean by a Custom Domain Name?
Custom Nameservers are available on Business and Enterprise plans. If your ns1 and ns2 records are for a subdomain or for other domains hosted elsewhere, then they are just regular NS or A/AAAA records.