When you are happy with each led position, ensure each marker sticker is firmly in place and remove the figure from the base. Although using stickers to mark the positions isn't essential, regular visitors to the site will know that this is my preferred way of doing this task. Firstly it provides an easy visual reference, and secondly - perhaps more importantly - helps provide a "key" for the drill bit.
To drill the holes, first pre-drill each hole with the 2mm drill. The final diameter for each hole needs to be 5mm, but don't attempt to drill this in one go using the 5mm drill - you risk splitting the plastic base. Take your time, and using the 2mm drill, pre-drill each hole using the weight of the drill itself as the downward force. When done, widen each hole to 5mm diameter.
Don't be afraid to connect the battery to the light kit, and position the leds underneath the model to experiment with the different lighting effects that you can get.
Remember, as with all the projects, this is your model build - and there isn't only one way of doing things.
Try your own ideas and experiment with different effects!
A great tip to make positioning the lights easy - ensure the model is in the correct place, and then use either a pencil or screwdriver to show where on the model each led light beam will hit. For example, the warm white led is to illuminate the figures face, so position the pencil in front of the figures face, running down to the base, to get the most accurate placement.