First of all I would like to say thanks to anyone who is willing to give his/her insight/opinions in advance

I'm after a bit of advice as to what to do next really.. We've already been denied once and we really don't have the resources at the moment to keep throwing money away

Background info:
I am a British citizen and my partner is a Filipino citizen with 2 months remaining on her VISA (Residence Permit - Leave to remain). Our baby is a british citizen by birth.
Here's the story:
Me and my partner have been living together for nearly 2 years. We first met Sept '08. We moved in together Feb '08 and had our baby daughter in Nov '08.

Now, seeing as her VISA is due to expire in Feb '10, we passed an application for an extension of stay back in October '09 and got denied

We recently got a civil partnership a couple of weeks ago.
My questions are:
1) any idea why the first application got denied?
2) which VISA do we have to apply for her?
3) WHEN is it acceptable and proper to submit the application -- seeing as her current VISA is still valid but we don't wanna leave it too late.
Please help

a) it's gonna break up our family
b) our daughter heavily relies on her for breastmilk -- she's allergic to milk, cheese, eggs, etc.

c) it's gonna be a huge expense
Any thoughts would be much appreciated
Thanks
Kel