I have a fair bit of experience delivering WLC to RICS via One Click. For a RICS calc, I mostly only use One Click for A1-A4, B4 and C1-C4 outputs. I then export the data to excel and complete the rest of the RICS process manually as One Click is not yet perfectly set up to deliver it (i.e. there are various steps required by the assessment methodology that you cannot yet take in One Click). Most answers to your questions are in the RICS document.
Your operational energy data should be taken from the most robust methodology available - this should really be an advanced DfP energy modelling process such as CIBSE TM54 which captures both regulated and unregulated energy consumption. Part L outputs are ok but only so long as you very clearly state this is what you have used. Industry is now well aware of the restrictions and issues with Part L, so by using it you actually skew the proportional embodied-operational split in a building, where this should be as accurate as possible. You need to know energy consumption over your RSP from the different fuels and apply the correct carbon factors. You can then use RICS Section 3.4.2 to find the NG FES document, estimate the diminishing carbon factors over time and apply this as your separate decarbonisation model.
For water, what Vasilis said. Otherwise you can use the Better Building Partnership’s REEB Benchmarks (released earlier this year), which will allow you to estimate average water consumption. These are actual water consumptions from POE based on hundreds of assessed buildings of various types and give ‘standard’ and ‘good practice’ values which can be used. Search online and find the UK Gov carbon conversion factors for water supply and treatment, and then a bit of research will give you an idea of proportionally how much water is removed from the building. You’ll then have all you need.
Joseph’s model for site operations seems like it would be the most accurate, based on a more detailed assessment of site activities. However, if you don’t have that to hand or are in early stages, use RICS PS Section 126.96.36.199 which tells you how to calculate. You don’t input this to One Click, its added separately. Cost plan is one of the most critical items for a RICS PS assessment so you should be able to make this estimation in accordance with the calculation rules fairly easily.
Hope that helps.