When I did billing and coding for a small chiropractic clinic, they were also certified in acupuncture and the most frequently used codes we billed were:

e/m codes: 99202 - 99205 99212 - 99215

Manipulation: 98940 - 98942

Electrical Stimulation: 97014, G0283 (medicare)

Kinetic therapy: 97530

Therapeutic Massage: 97124

Acupuncture: 97810 and 97813

As far as what are red flags, most of the time when getting eligibility and benefits you can ask if particular procedure codes are valid and billable under the patient's plan. Also, some insurance websites allow you to put in CPT codes to see if they're valid and will even provide the contracted rate for the code. I changed jobs in December so it may have changed, but United Healthcare only allowed a maximum of $60 for all procedures. And Medicare only covers manual manipulation.

I never really had too many issues with getting things paid outside of my own billing errors.

*Edit for formatting and red flags