Multi locus directed analysis for developing plant barcode.

I am working on land plants, and have just started my barcode activity. As by the recent publication, the multi locus approach for developing the barcode seems to be the most accepted procedure (though debatable). My query is: If i have sequences from two and more locus (which are probable barcode locus) and I aim at getting a evolutionary or/and phylogenetic relationship between species based on a combination of these locus, what should be the methodolgy to do so. Should the distance be computed for the different locus and then added and normalized and then using UPGMA or NJ one can have the tree. Or there exists a well established protocol for this acivity. Kindly help me as I am naive to this.