Which guidelines to follow are typically a business policy decision made by your employer.
For example, 99000 may be correct, but that does not mean an insurance company will pay for it separately. Any coding tool, whether software or even the NCCI list, will be the CPT or CMS guidelines. Insurance carriers come up with all sorts of rules/guidelines above and beyond those.
Many employers will also build additional payor rules into their billing software to help with submission of clean claims.
For example, you code a claim based on CPT guidelines, but the billing system software recognizes the payor does not recognize/accept the codes provided. One such situation could be consult codes. Medicare (and now most commercial carriers) no longer recognize consult codes. The claim you are coding meets the requirements of consult 99244 and that is what you enter. The software might alert you on the spot, or sometimes in overnight edits that the carrier does not recognize consult codes and instructs you to recode with new/established. From my experience, this is not something any coding software will alert you to (with the possible exception of CMS guidelines like NCDs, etc.) With my employer, the rules run overnight and there is a separate team that specifically works the overnight edits. Not my favorite system because the person coding will never even know it hit a carrier rule, in order to possibly remember for next time.
Unless you always code for the same carrier, I don't think employers would expect you to know each rule of each carrier.
I hope that helps better explain it, and you may need to ask your employer about their own policies and systems.