You should be able to check if you still have the 25k pots installed, the ones EMG use are typically mini pots, with a serial number stamped on the side that ends in 25k. My guess is, if you didn't explicitly ask for new ones, they may well be in there still, although if you paid for installation, the tech should have known better and informed you.
Normally I'd say you should be fine with most quality 500k-550k guitar pots, I've always had good results with audio taper CTS pots, whether BKP OEM ones or the premium 450 series.
One caveat though; guitars with emg mini pots need the shaft holes reaming slightly to accomodate larger standard sized pots. Assuming your guitar has the mini pots with smaller shaft holes, you can either have the holes reamed (which is a simple job, but can crack/chip the finish if it's done incorrectly), or you can source some good quality mini pots like these:
https://www.wdmusic.co.uk/electronics-c17/pots-c69/cts-guitar-pot-550k-mini-split-shaft-audio-taper-pot-with-9-tolerance-p365. You should be able to source these from most guitar electronics outlets. It's worth saying I've never used those myself, so can't vouch for them personally, although CTS pots in general have always served me well.
Without knowing your exact guitar and seeing inside the cavity, most of this is hypothetical, but I am trying to cover most of the potential bases.
If you are not sure, you can always post some control cavity images. As far as the configuration, two volumes and one tone is a common setup, although ultimately it's mostly a preference thing. If you are not sure, or just indifferent, I'd keep it simple and go with 2 volumes, 1 tone and a 3 way, if that is what your guitar is routed to accomodate.
Finally, I'd make sure the bridge is properly grounded, i.e. a wire from the bridge to a common ground point, typically the back of the nearest pot in the cavity. EMG pickups aren't supposed to have the strings grounded, but guitars which come stock with them almost always have at least a taped off bridge ground wire in the control cavity ready to be connected.