How to take water-dispersed PEDOT:PSS and disperse it in an organic solvent?
Even if you switch to an organic solvent, if the polypyrrole is in water, it will perturb the PEDOT:PSS layer.

Your best bet would be to use a poly-alkyl pyrrole or other conjugated polymer that's soluble in something that doesn't dissolve PEDOT:PSS.

Let's say you switch the solvent to DMF or DMSO and it dissolves the PEDOT:PSS. Then you spin-coat that new mixture onto ITO. Once you drop the aqueous solution of polypyrrole, it will dissolve the PEDOT:PSS.

I think you're looking at this the wrong way. Rather than trying to change the PEDOT:PSS (which will be tricky - PSS is anionic) you should consider changing your polymer. Alternatively, get rid of PEDOT:PSS and use another hole injection layer. (PEDOT:PSS is acidic and will etch the indium out of ITO.)