The base mon is the one whose evs get used in the fused mon. For example, if you fuse Zekrom and Kyurem, you get Black Kyurem. Black Kyurem is still Kyurem and as such, whatever evs Kyurem has will be what Black Kyurem has
Forgot to mention, it's not just evs. Also nature, hidden power, blah blah blah the base mon has will be the one that the fused form will retain. The second mon like Zekrom or the horsies are basically enslaved and thus have next to no influence in the fused form's stuff
Source: Experience