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Well gd2 and imagemagick are comparible if your using gd2 2.028 only drawback I see is in processing larger images with gd2 you will see more PHP fail issues because of the fact like stated it does use PHP memory. On alot of installs this PHP memory is 8mb so its good you have yours higher. However as noted trying to process huge files like a 17mb file and uncompress it and handle the images you can see that it will use 40mb of PHP in a snap.
Now the usual paths to mogrify are as such
/usr/bin/mogrify
/usr/local/bin/mogrify
/usr/X11R6/bin/mogrify
You can check with your host on exact location if it is present on your system or if you have SSH sign in and do a whereis mogrify.
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