Unfortunately you're going to need to let your knee rest and heal before trying this again. If you can put the flat pedals back on and ride without pain for the time being, that would be ideal, but if you can't, then just rest. You don't want to aggravate it.
Next time you go to try the cycling shoes, bring the tool you need to adjust your cleats. If you pay close attention, you should be able to feel which direction your knee is getting torqued, and adjust the cleat accordingly. If the pain is in a particular part of your knee right now, before you even start, try turning the cleat just slightly so that next time your knee won't be turned so much in that direction. Small adjustments, little by little, ride a mile or two before you make the next adjustment.
Also consider the possibility that the stack height of your cycling shoes and pedals is different from what you had with the flat pedals and whatever shoes you wear with them. You may need to raise or lower your seatpost as well.
A good fitting would be ideal, if you can afford it.
Speed comes from what you put behind you. - Judi Ketteler