So Sonic Frontiers is broken up with three main hub islands, which are all mini sandboxes of sorts. They have their own currency, their own collectibles, and unique levels/bosses. Your job is to collect gears, which unlock levels, which unlock keys; then collect emeralds and other bobbles that eventually unlock a boss. It's a lot of unlocking.
It's here, in these bigger higher-stakes confrontations, that you'll be able to morph into Super Sonic to fight. The catch is that generally, you have a limited time to be Super Sonic, and if you run out of time (denoted by rings, which count down), you'll be squashed by the boss.
Here's a few quick tips for playing as Super Sonic and fighting bosses in Sonic Frontiers:
Go into each boss battle with as many rings as possible. You'll want to get a handle on the first boss with roughly 150-200 rings.
If you don't have enough or find yourself constantly dying, you can quit, and load your auto-save to restart right outside of the boss arena.
You're always hovering as Super Sonic, so you can use the L2/LT rapid-fire kick ability constantly to your advantage without stopping/touching the ground.
As soon as an enemy draws back to strike you, hold L1+R1/LB+RB at the same time to parry, then counter-attack when the in-game prompt pops up on the screen. It's one of the easiest ways to deal chunks of boss damage.