[baikuza]

let see, if it is amino acid RCH(NH2)COOH
amino acid govern zwiter ion. so,

RCH(NH3+)COO- -->RCH(NH2)COOH
RCH(NH2)COOH -->RCH(NH3+)COO-

Do you simply have to pick various atoms as the "central" atom and apply it to the atoms that surround that atom, then move to another one?

VSEPR is used to "uncover" the molecules. i mean it is used so that we know what kind of shape it is. is it tetrahedral, or trigonal, or trigonal bipyramid....etc

so i'll said you can analyse the structure of the compund. all of them. in the case of amino acid, the general structure is RCH(NH2)COOH.
then i'll said the central atom you should look is RCH(NH2)COOH.
it is tetrahedral. 4 sp3 bondings. and has no lone pair electron so it is 109^0

VSEPR can be used to analysis the shape of compound.
if it is Lysine. take a look at this http://en.wikipedia.org/wiki/Lysine
the carboxyl group is trigonal, and C which bond with amine group is tetrahedral. the other C, is the tetrahedral.
NH2- govern trigonal. blah..blah.. too much (warp)

so. you can use it for all.