I have an older Skeeter and was refering to mounting the Bas pro shops charger on a transom brace not actually on the transom

PS thanks all for the info

  I mounted my CSI unit (waterproof, and recommended) on the cover over the bilge. I would avoid putting any fasteners into the transom...if they leak, and if you have a wood core transom, it's trouble. I don't know what kind of boat you have, or what charger you bought.  If one corner cannot be bolted down, maybe a spacer and longer fastener would help, or a bracket of some sort. More info would help.

Hey Jim, as I know the operator well, I believe it runs on METHANE!!.....Should work well!

Of course it's electric.   I said electronic vs. the type that use coils and transformers internally.  These types of on-board chargers are often refferred to as "Traditional" chargers.  They will work fine, however they are heavier, generate more heat, and usually don't have the number of charging stages that an electronic type has.  This factor can often affect the total charge a battery actually gets that reads fully charged.  It also can affect the lifespan of a battery.
There is a good article in Bass & Walleye Boats magazine this month about the different brands of chargers on the market.  They tested 7 different ones and the results are surprising, to say the least.

This is an electric charger. I plug it in  and there are no squirrels involved so it has to be electric right?

Probably because of the heat rising around the unit.  Electronic type chargers, which don't generate as much heat a conventional charger style, can be mounted in any position.  
Examples of these types are Guest, Stealth, and Motorguide

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They dont recomend mounting upside down. I am not sure why

How about on the underside of the compartment lid? ???

I think I have found a place to mount it but I have to get creative, as a corner of it will not be attached to anything

I would find a place on the transom or a compartment wall as the two you mentioned do not do well with heat and or electricity!  Mine is on a support structure with little to no movement.

I just got my onboard charger from bass pro shop's and I am having trouble locating a place to mount it.

The best spot that I could find in the battery compartment is either on the side of the battery or on the gas tank neither of which is an IDEAL place. has anyone come into this problem? they say to mount it horizonially or vertical with cords down. any help?

Jim