For wheel bearings, fully sealed is a good way to go and probably the best choice.
Hard to believe they sold you sealed bearings for the engine though. My first thought was that you should be able to remove the seals and clean out the grease, allowing them to be lubed by the fuel-oil mix as usual. On second thought though, I would wonder about the suitability of the bearing they sold you to be used by this application. A general industrial bearing (which is what it sounds like they sold you) might not have the tolerances, finish, and speed rating of correct crank bearings. After all, crank bearings need to spin up to 10,000 rpm. I'm not sure the bearings they sold you are up to that demand. I personally wouldn't take the chance. Buy some correct bearings from rockymountainatvmc.com or ebay (get name brand), or just buy some factory Yamaha from your dealership. A lower end is a terrible thing to waste....