You really need to consult your own tax professional now, and should have done so before paying anyone out of your own pocket. I would imagine that--depending on the formal structure of your company (e.g. DBA, sole proprietorship, partnership, LLC, or Corp) or lack thereof--how you put money into the "company" from your own pocket can have wildly different tax implications, just as how you take money *out* of your company has wildly different tax implications. For both you as an individual, and for your company.
In particular, I'm 95% certain that putting your personal wages into a "company" wouldn't adjust your income unless, potentially, it was somehow structured as an investment. I certainly would not expect for your employer to adjust for it.