I am doing honeybee studies and need to dissect out the hypopharyngeal glands, salivary glands, and if possible the corporum allatum. Is there a detailed protocol (preferrably with images) of how to dissect these structures?

Well, you are not likely to find written instructions for these dissections. However, excellent digrams or plates of the salivary and hypopharyngeal glands can be found in Anatomy and Dissection of the Honeybee by H.A. Dade (publisher: International Bee Research Association; ISBN: 0900149981). Also, Zachary Huang at Michigan State University has photographs of some of these glands on his bee anatomy page.
The corpora allata are much tougher to dissect and locate. Let’s start with the salivary and hypopharyngeal glangs. The easiest way to dissect them is to decapitate a bee and place the head onto a wax surface, such as a Petri dish containing beeswax. Then anchor the entire prep by placing insect pins through the center of the compound eyes (1 pin per eye). Once secured, use fine micro-scissors to cut the face from the rest of the head. To do this, start at the frons near the base of the mandible and cut along the inner margins of each eye all the way to the top of the head near the ocelli. When both sides are cut, the face can be lifted from the head, BUT before removing the face, the antennal lobes will have to be cut from beneath the face. To do this, lift the face near the frons, insert the scissors and try to cut the antennal lobes free of the antenna. They will make a “snap” sound when cut. As the face is lifted, the hypopharyngeal glands may appear as yellowish-whitish tan glands on the surface of the brain. They may be underdeveloped in non-nursing bees, and in these cases, they appear as shriveled strands. The salivary glands project posterior to the brain. The mandibular glands are within the mandibles.
The retro-cerebral complex in honey bees consists of the corpora allata (CA) and the corpora cardiaca (CC). The CA stores and releases JH III, and the CC releases several horomones including PTTH, which ultimately stimulates ecdysteroid production. This is hard to describe, but you want to look at the area where the esophagus comes closest to the brain. This endocrine complex sort of encircles the esophagus here — but these glands are relatively tiny. However, they sort of have a tyndal bluish tinge to them, and with practice you can consistently find them. I recommend that you locate these glands in something larger like a house cricket, and once you are satisfied with your ability to find it, switch back to honey bees and give it a go.
– Jeffrey W. Harris, USDA-ARS