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Ewww ... big questions, which I might take to email later on the fine detail. But here goes:

When collecting for science (as opposed to for 'pretty displays') there are only usually 2 things to think about:

1. protecting the specimen in the best way possible in the short & long term
2. preparing the specimen so that it can be identified as easily as possible

With each group of insects you may discover different answers to those questions, depending on how hard/soft the specimen it and which features the identification keys use. Some keys/groups assume that specimens are preserved in alcohol (eg. spiders / molluscs) and others assume they will be dry (eg. most insects). I will assume we are talking about Diptera & Hymenoptera. Also, please remember a lot of this is my personal preference - others might/will disagree!! :)

I pin most specimens on their sides (lateral pinning) with very fine micro pins; diagonally so that I don't destroy the same feature on both sides. I then make a 'stage' using a thin strip of plastazote (high density foam rubber) and push a thick (size 3 or above) 'continential-sized' entomological 'stage-pin' through one end so the stage sticks out perpendicularly. The micro pin is then pushed firmly into the foam stage.

This method protects small/medium specimens very well while displaying as many features as you can. The stage-pin is strong and easy to hold/manipulate when moving the specimen and the stage absorbs most vibrations.

Also, this method lends itself very well to bulk-collecting of groups that take a while to identify. I will go out for a day in the field and catch maybe 50 insects. I pin them with micro pins and immediately put them in a clear plastic box with a sheet of foam at the bottom and 1 label containing all the data for that group of insects. Then when I have time to identify them I put a specimen on a stage; identify it; and put the specimen's labels (copy of the data & a seperate label for the name) on the big stage-pin, under the stage.

You can direct-pin, 'top-down' (dorsally) but I only do this with very large specimens (eg. Tachina spp. or bigger). Also, with hymenoptera many people prefer gluing the insect to card but I feel that very fine micro pins are much easier to use (glue is very messy); allow for moving later (glue can be dissolved but it isn't easy); need not destroy much/any surface features; and in general I like to have 1 mounting method for all my specimens.

As I mentioned, I use the flat, clear, plastic boxes for pre-identified specimens and they keep everything clean and dry and take up very little space. But when staged the specimen goes into a larger wooden store box. As long as they are kept indoors and dry they should be fine. If you are worried about pests getting in and eating the specimens you can always freeze them for a week or more in a household freezer. Many museums do this as a matter of course as many insecticide chemicals (napthalene etc) are now banned.

I arrange identified specimens taxonomically down to sub-family and then alphabetically there after. But with larger collections you might want to group by tribe too.

I'll email you some photos of my collection here so you can see. Oh, and I don't know why bacteria can't eat insect chitin :)