IF you use the flush, you have to be mindful to get it all out of the system. If your antifreeze smells like ammonia later, you know you still have leftover flush in the system.
I'd check over the radiator, water pump, hoses and replace if they looked questionable. I'd also change the thermostat.
If the coolant is quite dirty and scaly then the radiator probably doesn't look so good inside. It can be easier to replace the radiator than try to clean it. And if its old, it can crack and leak at the first cold snap in the fall and who wants to be changing radiators when its 30F outside.
If parts look old and original and you plan on keeping the Jeep indefinitely I'd just change it all.
Good maintenance is changing the coolant and thermostat every 2 years. Use distilled water available at Wal Mart or the grocery store for less than $1 gallon.