In the US anyway a patent is usually granted to an individual or individuals in the case of co-inventors.
What generally happens if the inventor is doing it as an employee of a company is that he/she assigns the patent rights to his/her employer.
In your case since you will undoubtedly be using a patent attorney you should seek his advice.
Probably the best way to proceed is to get the patent in your name and leave it at that until such tine as you seek outside funding for your company. At that point it is virtually certain that the outside investors will require that the company have rights in the patents as a condition of their investment.