Hi, I'm using this Annexin-V-FLUOS staining kit and according...

Does this number represent the initial amount of cells that have been seeded or for the ones that would be harvested?

Yes. It represents the initial amount of cells that have been seeded

Second question; how will the percentages be affected if I use less amount of staining mixture?

For us it has worked very well for the mentioned concentration, if you want to use less amount of staining solution, we would recommend seeding less number of cells.