When I switched to amsoil in my 06 and both of 99's and my 97 I only left a little cat oil in the tank and then filled them with amsoil that way I didn't have to bleed the oil pump. (no air in the line is a good thing). as for my daughters 04 zr120 I just took out the drain plug and let her run then toped it off with amsoil.
I agree with Dad ... run your oil down to the point where you need to add oil. Then just top it off with the Amsoil. No need to empty it out at all. And yes, the Amsoil will work just as good or better than the APV oil. Also, you may want to calculate your fuelil ratio again and set your oil pump accordingly.
Which AMSOIL do you plan on running? Check their site to see what they say. The quote below comes from their site regarding their HP Injector Oil. Note the bold text.
"Use as injection oil or as 50:1 pre-mix (2.6 oz. per U.S. gallon of gas) where NMMA TC-W3 or API TC oils are specified. Compatible with mineral and synthetic TC-W3 type two-cycle oils, however, mixing two-cycle oils should be minimized."