Projects are billed individually. Upgrading the plan for one project doesn't upgrade the others, so if you choose to only upgrade 1/3 projects, you'll only pay the plan price of 1 project (1x25 = 25) while the others will remain on the free tier.
Likewise, if you upgrade 3/3 projects, you'll pay the plan price for 3 projects (e.g. 3x25 = 75)