For the Booleans problem, ensure that both polys are 'sat' inside each other or the poly for some reason do disappear.

For the merge poly's tool, click the option box next to the merge poly menu then alter the slider distance as this controls how close the polys have to be with respect to each other before they merge, basically so you don't merge hald of your model together without realising it and believe me its easily done.

As for rigging I'm currently learning that myself so unfortunately I cannot help you other than suggest buying the low poly bundle in the DVD section here like myself or 'google' free maya rigging tutorials, though most of the links are dead that I found.

Hope this helps.