You profille says you have a 88 XJ, is that correct. Wish people would just say the year of their rig, helps the guys helping you out.
If you have the stock cooling system then you have six sections of heater hose. Supply:
1) thermostat housing to heater valve
2) heater valve to upper hole of pressure tank
3) heater valve to heater core
Return:
1) heater core to "Y" fitting
2) Lower pressure tank fitting to "Y" fitting
3) "Y" fitting to pipe screwed into the water pump
I learned the hard way the parts catalogs have the wrong valve listed, someone screwed it up and the mistake is propogated. Go look at ACDelco.com and look up the heater valve for your XJ. They use to list only the correct part, then the got "infected" and listed both. I hope for your sake they still list both, take those print outs to the parts store and show them you want the valve wit the 3 hose nipples on it, NOT a valve with 2 hose nipples on it.
If your XJ still has the aluminum bands on the "y" fitting and heater valve the I strongly suggest you go to the dealer and buy all 6 sections of heater hose in the next week. Replace them all at the same time, those hoses will be 16 years old. I learned the aftermarket just does not have proper fitting hoses for an 88 XJ heater system. Tried them for 2 years, went back to dealer hoses to make the underhood look better.
Hope the routing and valve info helps out. CraigH has a good heater core flush and heater core flushing was posted in the past week or two on here, do a search. Flushing the core will get you more heat!