You can use more or less the same protocols for parts or whole insects, with reducing the volumes and perhaps longer incubation times and better homogenisation to increase yield (depends how much DNA you need finally). Anyway you also might consider protocols for DNA extraction from museum species without damaging the specimen, so that you can use the whole fly.

Here's one example:

Gilbert MTP, Moore W, Melchior L, Worobey M (2007) DNA Extraction from Dry Museum Beetles without Conferring External Morphological Damage. PLoS ONE 2(3): e272. doi:10.1371/journal.pone.0000272

Dear Peter,

Thanks for your answer & suggestion.

Fartyal