NOTE: You must be signed in to your Minecraft account with a rank added to your account to purchase a Rank Upgrade, and you must be online on the server upon purchase.
Bonus benefits clarification: Because you're upgrading, you only pay for the difference in between the rank you currently have and the rank you're purchasing. All rank bonuses reflect that.
For example: The Super Trainer rank grants you 3 Shiny Non-Legendary Pixelmon Tokens as bonus in total. Trainer+ grants you one shiny token. Upgrading from Trainer+ to Cool Trainer grants you another (2nd) shiny token. If you then upgrade from Cool Trainer to Super Trainer, you've already received 2 shiny tokens and shall receive your third token, making you have 3 tokens in total once you have the Super Trainer rank.