WINPCnc and drilling operation

Hi,

Im new to cnc and we have started our first tests with milling (with some success). Im using Estelcam and it seems to produce great results. We are testing pcb milling (so I use Eagle > Inkscape > Estelcam > WinPCnc ). Now there is few newbie questions I still havent figured out (yet tested in practice):
1) What is best way to use different tools for one job? (milling and then drilling)?
a) Is it better to first turn off drilling tools on toolbar and run just milling part (am I correct to assume - thats how it works? turn off tool and it skips part in code????), and then separately each drilling part (with different tools)?

b) Or run it at same time (havent tested yet - what happens when tool change need to take place? [seems I found setting at Parameter which affects this] - regarding this - what about leveling tool?

Edgars