Hi Carl
Depends on which bait you are using.
Most will respond to microwaving. Unfortunatly trial and error is the only way to find out for sure. Try ten second bursts untill you find out the optimum cooking time. A good tip is to drill an hole through the boilie first and place a cocktail stick through the hole wilst cooking. This is done because microwaving usually leaves the bait very hard and brittle. Trying to drill the bait after cooking usually results in them splitting. When baits are prepared in this way a lot of the flavour is burned off. Many anglers like to glug their micro popups with a complimentary soak, to help negate this affect.
One company sells an insert kit, I think it may be Gardner could be wrong. Whith this, a tool is used to bore out a cylindrical section out of the centre of the boilie. The portion of boilie that has been removed is replaced by a piece of cylindrical foam. This foam is supplied in various colours to compliment your bait. Cannot comment upon how well this works as I have never had the need to try one.
If all else fails why not just put a cork ball above the boilie, ala snowman style. It does not look pretty, but I have seen no evidence to suggest that it is less effective than any other method. I witnessed a twenty six pound common caught on such a rig. From the north west I should hastily add. Good fish in our neck of the woods.