I am currently in the process of applying for a Phd

i've applied at the same university where I am currently doing my masters degree, the phd supervisor involved is also the course leader for my masters.

I haven't heard anything back yet (he said soon), but I wanted to apply for a different type of course based another university.

the problem I have is that one of my references is my potential supervisor/masters course leader!

i'm just a little stuck at the moment as i'm still waiting on the phd, and if I apply for the second course before knowing about the phd would that cause some problems?

if anyone has been in a similar situation it would most appreciated.
Many Thanks