HOW DO YOU RESOLVE BIG PROBLEMS IN HOW TO RUN A COMPANY WHEN IT IS
OWNED 50/50. IT INVOLVES PAY RATES

You dissolve the Partnership.

Most 50:50 partnerships come unstuck for some such reason.

I suggest that the two owners call in a mediator, someone savvy about
pay rates and who can discuss the economic ramifications for the
company from the owners' viewpoint. I am assuming that the partners
both have a great interest in the company, want it to be a success,
but have run into a single problem that they disagree about.  They
need an objective and trusted third party to help them get
around/through an impass, help each of them to "uncement" his thinking
and maybe back down from a position taken that he cannot give up in a
continued one-on-one confrontation.

Seperate the whole management by two and never involve another's dept
by one. This will keep 2 partners happy and busy. No other problem
will occur.