Hi @sam-smcarpentrys
First of all, do you have CIS Switched On?
Turn on CIS in QuickBooks Online
Unless you've created your own Product/Service (with CIS Deduction) you should use the one(s) that QBO creates - I think it's something like CIS Labour Standard (20%).
Materials can also be added (CIS Materials with no deduction).
I don't know how this will appear on a standard invoice template - you may need to look at that or design another template if you also have non-CIS customers.
Using VAT Code RC CIS on all lines will apply the DRC VAT.
QBO doesn't (I think) show anything on a standard invoice template to advise the customer that DRC has been applied - you should add a message to your invoices.
Something like...
* Domestic Reverse Charge VAT applies to all items on this invoice. Customer to account to HMRC for the reverse charge output tax at the relevant rate.*
Hope this helps.