I have an S-Corp and brought on a CEO in 2018, but as the company made no income I made the mistake of not paying him a wage. Is there a way to settle this retroactively?

A few comments here based on your facts:

1. If you aren't generating any income, it is doubtful that you are making any distributions either.  The wage vs distribution is a hot topic for S corporations that are making $$ and instead of paying wages, subject to social security, the S corporation is making distributions which are not subject to social security tax.
2. So keep this in mind going forward.  You need to be able to show, if audited, that you are paying working shareholder's a reasonable wage and not just paying out distributions..  This is a hot issue for the IRS.
3. The real issue here is how you treated the issuance of the shares of stock.
1. Did this individual purchase them?
2. If "yes" was a valuation done on the company to justify the purchase price as being FMV?
3. If the shares were just "given" to this individual, then the FMV of the shares is compensation to this individual.
4. If after reading the above you still believe that this individual was under compensated, then just make it up in 2019.  Of course, this all depends on the earnings of the business and cash flow.
5. Also keep in mind, that certain tax-free fringe benefits available to C corporation shareholder's will not be available to this individual since they are a more than 2% owner.

Yes, when I brought him onboard we did handle the stock issuance as a purchase based on the same purchase price I paid when the company issued stock to myself (when the company was founded a number of years back).

The stock purchase was for a little over $1,000. So I was incorrect in stating the company had no income, the only income the company had was his stock purchase. Expenditures for patents and other business expenses was well over $20K so the company is not making any money.

With that said I still have these questions...
1.  Where in TurboTax Business do I enter the $1K income from stock purchase? Should I just make my own category under Product Sales?
2. How do I handle his lack of wage/distribution (TurboTax is warning me about audit risk)? Do I make a small distribution retroactively to cover the small amount of time he participated in the company? As I mentioned he has only really been on a handful of conference calls and is not tasked with any real work or deliverables.

Thank you so much for you help!

Follow-up to your comments:
1) The $1,000 paid for the stock is not income.  It is a capital contribution.  This assumes that this individual in fact paid this amount.
2) Based on your facts, it does not sound as if you have really started your trade or business.  It appears that you are still in the start-up phase.  
3) If that is the case, then all expenditures are capitalized as either start-up costs or organizational costs.  These can be expenses or amortized once the business begins business.  See the attached link that provides an overview of this area:<a rel="nofollow" target="_blank" href="https://www.thebalancesmb.com/how-to-deduct-startup-costs-on-business-taxes-397608">https://www.thebalancesmb.com/how-to-deduct-startup-costs-on-business-taxes-397608</a>
4) Based on your facts and follow-up comments, as I stated previously, I don't believe you have started your business.  As such, everything spent at this point is either capital contribution or capitalized as a start-up, organizations, or capitalized in some other category.  You will be able to start amortizing these expenses once you begin your business.
5) If you have not started business, then your 1120S should only include a balance sheet and nothing else.
6) Based on the facts, I would not worry about the salary matter until 2019.

Thank You!!!