[CrimpJiggler]

I'm reading about ion chromatography at the moment and read that one method is to use an ion-pair reagent which pairs with the ionic analyte, forming a neutral compound which can then partition into the non polar stationary phase. If an anionic analyte pairs with a cationic ion-pair reagent to form a salt, how would it be any more likely to partition into the non polar stationary phase? Salts are still ions. For this to work, does the analyte have to form a covalent compound with the ion-pairing reagent or at least a salt which is insoluble in the mobile phase?

[Arkcon]

You are very close to figuring it out.  No, a covalent bond doesn't form between ion pair reagents and the analyte, it is simply a strong association between two charged molecules.  Under typical reverse phase conditions, they associate more strongly, forming something like a neutral salt.

Consider the old simple laboratory experiment, where you separate an organic amine, an organic acid and an non-polar organic compound, by shaking an solution of them all in an organic solvent, first with aqueous base (to convert and extract the organic acid into a salt), then with aqueous acid (to convert and extract the organic base.)  Ion pair chromatography is something like that, but making a looser association, and making a charged species more non-polar, and instead of shaking, a linear series of extractions down the column.