The original remote should be used only to teach missing commands (and for confirming the dataset when the device supports multiple addresses). When using the Software interface to configure you Harmony remote, forget the original remote (put it away), and select the appropriate command(s) from the drop-down list (the window with a tiny v). Don't confuse input label names with command names. Also remember the Harmony interface is very infantile. Put your thinking hat on - think outside this infantile box - read between the lines.

So for your main TV device Adjust Input Setting, select Method 2, then edit the input list (label names) to show only HDMI1 and HDMI2 (you can add more inputs later once you understand the concept). On the next page, it will ask what command to use for these 2 inputs. On the left is the label name, and on the right is the actual command name. So for input label HDM1, select command "InputHdmi1" (from the drop-down list - click the little v), and for input label HDM2, select command "InputHDMI2".

For your Clone TV device Adjust Input Setting, select Method 1, edit the input list (label names) to have only "Analog Tuner" and "Digital Tuner" in the list. On the next page select no (you don't skip input). On the next page select the command named "Mode". On the next page select "Stays on whatever it was when it was turned off". Note: Based on your reply, the TV tuner toggle command is named "Mode". I would have never guess that one. Now you see why I was confused with your usage of the original remote button names and the dataset command names.

Note: The activity input setting goes by the label name. So for example, in your Watch DVD activity input setup, select HDMI1 (label name). The activity configurations are like high level managers and the device configurations are the grunts.