first get the correct touch up stick for your car (you will need the paint code do a search on here its location is bound to have been mentioned)
next use a pin or needle to pick out and remove all the rust
next clean the area with something like Isopropol alcohol or Methylated spirits
now shake the colour stick well and apply the paint thinly (build up the layers allowing it to dry in-between coats so its a fraction below the level of the paint.. and allow to dry well
next apply clear coat touch up in the same manor but build it ever so slightly high then cut back once dry using a fine cutting compound such as scratch-x
tip for you paint it using a Pin or cocktail stick or engineers scribe as you have far more control than with the stupidly large brush on most touch up sticks