You won't get a completion cert for a structure that doesn't comply with the permission granted. Without a cert of completion you cannot occupy the property.
This is in relation to the Building Control Amendment Regulations, Planning is a separate matter. You will not need a Cert of Compliance at this stage as the full planning has not been implemented. You may be able to get an interim Cert to say that the first phase is in compliance with what has been granted, just incase for insurance reasons its required, but the Completion Certificate is a BCAR process.
Basically, you have planning for the development.
This is how you can proceed :
Lodge a Commencement Notice to the Building Control Authority online through the BCMS (
www.localgov.ie)
Depending on the floor area, you will need an Assigned Certifier or you can Opt Out of this requirement. You will need to engage an Engineer/Architect/Surveyor anyway to oversee, design, inspect and certify.
The Commencement Notice can state that the development is being carried out in 2 phases. The first phase relates to the Ground Floor Element, and then the 2nd Phase will be the First floor Element, which you will lodge a new Notice when that time comes.
The trouble here, is if you don't complete the first floor element, then you may need to seek Planning Retention to regularize what is actually built on the ground.