I have a G25 and have no problem at all with this. I use the H-shift for normal cars and the flappy-pedal-gearbox (courtesy of Jeremy Clarkson) for formula-like cars. Just assign the H-shifter positions to their respective gears in the options and then the flaps behind the wheel to the gear up (right lever) and gear down (left lever). The game will then automaticaly switch between the modes, depending on the type of vehicle you drive. Or you can choose manually to drive normal cars with the semi-auto gearbox if you wish to, but I don't do that.
The only problem with LFS+G25 is that if you want to use the sequential shifting on your H-shifter console, you have to reassign those gearstick positions to gear up and gear down, thus losing the flaps assingments. I just hope I am not overcomplicating things for you.