Will Worsdell

I'm self-employed as the Director of a Ltd Company. When I ran the first payment to pay myself through my limited company the PAYE figure was a negative amount, presumably due to me being due a refund from earlier in the tax year when I was employed by someone else. As I don't intend to pay myself more than the tax free allowance through my limited company I don't envisage ever having to make a PAYE payment to HMRC through that company. My question is how does my Limited Company get the PAYE refund from HMRC that it has already had to pass on to the employee (me)?