I've been using Torque and my Bluetooth dongle on my 2000 Ford for a while. I just got a 98 Ram this year and Torque will read the codes, but when I clear them, they don't clear, nor does the check engine light turn off.
Having a CEL means there's a fault. Fix the fault, and the code will clear. Just clearing the code with the adapter doesn't clear the fault.
You need to figure out what the code means, fix the problem and the CEL should clear itself.