as for toning up a bony body, try sticking to the weight machines at your gym. Alternate the muscle groups that you work out, i.e. chest and shoulders one day and back and arms the next. Try to do 3 sets for each exercise you do.
Afterwards, be sure to eat immediately after your workout. Your muscle tissue begins rebuilding itself right away so getting protein to it asap is important. If you haven't already, go to your local GNC or similar store and get a protein powder that you like. It will become your best friend.