So how does one actually use the tripod?

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Essentialy whilst I have used a tripod, geared head and focusing rail to good effect in macro, my main use has been either with 1:1, 1:2 or a little bit of 1:2 macro in the field - whilst my works (to date) with higher magnifications have always been in a more studio like environment where I have a still subject and the ability to control the subjects and the cameras position.

However I've been trying to use my MPE in the field with the tripod and its giving me a lot of problems. I seem to find it impossible to focus the setup effectivly on the subject - whilst if I shift to handheld I find it far far easier. I do want to be able to use the tripod since focus stacking gives the best results when done with a rail - and further my lighting is currently a flash on an offcamera flashcord and if I can't hold the flash up high I am limited to side on light only (as the flash rests on the ground).

So for those with more experience in using high magnification gear in a field what advice can you give?

For refrence my current tripod setup is as follows:
Manfrotto 055XPROB
Manfrotto junior geared head (does anyone else find the quick release plate with this tends to not have a very harsh grain and let things slip on it? I've also found the glue to be giving way at times also)
Ebay/HongKong/Adorama focusing tails (set of 2 rails though at present I tend to use only one for forward/backward motions)
 
I've tried that and its just not working for me. And I have been advised by some others to try using the tripod upside down.
 
And I have been advised by some others to try using the tripod upside down.
How's that?
My tripod use, when I did/do use it, is for portraits. First I frame it, lock the composition, and shoot it. I'm not an expert on macro, but when I did few macro in the past, it was done the same way.
Hope that helps.
 
Completely and totally ditch the tripod. Using a reverse-mounted 37-72mm Nikon Series E lens provides a rather usual lens that allows greater-than-life-size macro focusing, with variable magnification, much like the MP-E 65 does, which is great for things like ants, for example, and other very small things that allow the photographer to approach closely without biting, hissing,spitting, or fleeing the scene of the scene, so to speak (bad pun intended).

Yep, ditch the tripod and rely on moving the camera closer or farther away from the subject, and relying upon your flash illumination to "freeze" the motion blur that exists due to either subject motion, wind motion, or human breathing. As you have no doubt noticed, at 2x life-size and larger, the DOF is miniscule, and as the lens is focused closer or farther, there is what is called focus "breathing"...the tripod is really not helping you much is it? I think you ought to try ditching the tripod for many subjects, especially living ones, and instead set a magnification level, and actually move the camera to where the focus looks good, then Shoot! The success or hit rate will not be anywhere close to 100 percent, but without a tripod and macro rail fighting you, you will be able to set up faster, shoot faster, and get more chances than if you are fighting that doggone three-legged beast. If you need to do focus stacking, well, there's that tripod and all its issues coming home to roost. With your experience and devotion to macro photography I'll bet you will learn how to get more and more out of the MP-E as time goes on.

It sure is a cool lens!
 
For macro..... I tend to hand hold. Dem critters R2 dang fast for me.
 

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