I assume you have things set up OK. Subject against green background on one track and the desired background on a higher (lower numbered) track.
The success of a green screen effect depends foremost on the quality of the green background -- correct shade of green, even lighting, no shadows etc. If you (the subject filmed against the green) are partly disappearing you probably have some green component in your clothing etc. This might not be 'pure' green, but close enough to your background shade to be rendered transparent.