I don't need the analog inputs, so I should be able to disable them, does anyone know how you do what?
You don't disable them as such but just use them as digital. With 'genuine' Arduino, digital 14 is the same as analogue 0, etc. So to use analogue 0, you'd say pinMode(14,INPUT); and digitalWrite(14,HIGH) to connect the pull-ups.
In principle, you just need to set some bits in the appropriate registers to achieve what you want. In practice, this means you have to read the datasheet a little bit.
For anything like this, I make a really simple sketch where I read the register and Serial.print it bit-by-bit. I then change the bits (OR with 1 to switch on; AND with 0 to switch off) and print again to make sure I've only changed what I really want to change.