The IR dataset for you Samsung LE46F86BDX contains many discrete input and power commands. That does not mean you particular model will support them all. The dataset is by brand rather than by specific model. That is why you should try all the commands in device mode. Besides the discrete commands, you may find other "easter egg" commands leaving you OEM remote in the dust.
The Harmony is an activity based remote. View the activity like a high level manager. The grunts are the device power and input settings. It's the device input settings (not the activities) that determines how to switch input and what command(s) to use. You specify the desired input in the activity wizard. The wizard ask for an "high level" input label name (not a method, nor a command name).
The default device adjust input settings for your TV is already configured to use the discrete method (Method 2). On the left, you will see the input label names, and on the right you will see their associated command names. You may need to verify the behaviour of these commands in device mode. See my post #2 above.
The default device adjust power settings for your TV is configured to use the toggle method (one button for both) along with the PowerToggle command. I see the discrete PowerOn and PowerOff in the dataset. Test them in device mode. If they work properly, then reconfigure the power settings to use the discrete method (separate buttons for each) along with the PowerOn and PowerOff commands from the drop-down list.
Note: The Harmony configuration interface is very infantile. Read between the lines. It often refers to the OEM remote buttons. Ignore that, put the OEM remote away, and instead use the database commands from the command drop-down list (small window with a tiny v).
Once you are done configuring the devices, then create/modify your activities. Then use the activity Customize Buttons to add/modify the activity button mapping. You can map any command from any participating device to any activity key. The soft labelled keys are under the Addition Buttons tab.
