If I Suplex an enemy successfully and then whirling throw them (rolling a normal success) would they land prone because they started out prone or would they land on there feet?
Nothing about the throw seems to end the prone condition, simply apply it on a critical success.
Although, you could just throw them into the air and let the added fall damage auto prone them. At least until the gm throws a book at you.
Trip + Grab + Whirling Throw, however, is doable. Our table rules that a Prone target being thrown remains Prone since the target never used a Stand action to not be Prone.
Also, while Whirling Throw calls out landing prone on a Critical Success, it is silent about how the target lands on a Success.
Suplex will cause you to no longer have the enemy grabbed. Suplex, Grapple, Whirling Throw would be valid assuming that you have the target grabbed at the start of your turn.
Being successful at all three of those checks may be difficult. The first two will use and increase your Multiple Attack Penalty, but Whirling Throw will not use it, so you will make that check at full Athletics bonus.
And I also think that mechanically the target would remain Prone after being thrown (assuming the Suplex was successful). Nothing in that series of actions removes the condition from the target.