How to apply for a software patent that can be combined with hardware?

You can sign a contract with the software company first. Generally speaking, the patent right belongs to you, but there is no guarantee that any special terms in the contract will infringe your rights.

And what do you mean by software that can be combined with hardware?

Look at the description behind you, it should be a software. Software can be protected by software registration, and at the same time, it can apply for patent protection through certain methods, but the technical requirements are relatively high. I suggest you find a professional patent office.