I want to capture footage to 2 drives for editing in a Prem Pro 2 project. What is the best way to proceed regarding scratch disk allocation etc ?

Based upon the configuration in your tag, the two disks you have don't give you many options. I have four drives on my machine. Programs on the C drive. Scratch files on the D drive along with the system swap file. Video goes on E and F. 80GB isn't much room these days but it can work. I wouldn't load it too full as performance will suffer if a drive is too full.

If you have US$100 to spare, I'd recommend buying another drive for your scratch files.

Thanks Tripp,

I should have said the second drive with footage on it is an external drive ( F ) which has about 100GB free. The C drive is 4/5th full. Under Preferences > Scratch Disks I have Captured Video Path D and Captured Audio Path D. Am I able to mention 'and Path F' ? Sorry I'm a bit of a novice at this.

If the external is not eSATA, get at least 2 internals more. Your C drive is dangerously full, so it may well behave like a snail, that breaks before rounding a corner.