My primary job stills uses paper super bills, we aren't switching to EMR until next year, so we have used the same system for marking our super bills for the last few decades....
The first column and a half of the paper super bill are the CPT codes. The bottom half of the second column are self-pay supply items. The last column are all the ICD-10 codes. Using a highlighter, the doctor will highlight the CPT code she wants, then will draw lines with the highlighter over to the ICD-10 codes she wants used for that code. She does this for every CPT code she uses for that particular visit. We jokingly call it "roadmapping" in our office, because if she does a lot for one patient, there are lines all over the place, but it is very clear what CPT goes to what dx's. Then our front desk person enters the dx's into a certain area of the patient's case in the software, then enters the CPT codes one by one, making sure to check off the box/boxes for the appropriate dx's that go with that code. The way our software works is that all the dx's are listed at top of case, and are assigned numbers 1-12 depending on how many are on the claim, then when you type in each CPT code, there are 12 empty boxes next to the code which correspond to the dx's. You simply check the boxes you want, and that assigns the dx pointers on the claim forms. Our front desk person will also assign the appropriate modifiers, the doctor does not do that on the super bill.
I then check her work at the end of the day, and send the claims in, and I also work the rest of the revenue cycle, such as payments, statements, A/R, as well as provide any education the doctor needs to stay compliant, etc. Before we added another doctor last year, I did all of the this, plus entered the billings, but now I am rarely on the front desk. When we switched to ICD-10, I re-ordered our dx's codes on the super bill, so that often used CPT codes in the top half of the second column had the most used dx's directly across from them in the third column, and that has made things easier for everyone.
This is just our system, but it works like a charm, and everyone understands it completely. I know of other offices that expect the biller/front desk person to assign the dx's, or the doctor will just scribble them down somewhere on the super bill, and again, it is someone else's job to assign them accordingly. My doctor has been in practice for almost 40 years, so she is very up on coding, and likes to do it herself, which is really how it should be in an office setting, IMHO.