I am new to universal remotes and there is lingo I keep reading that I have no idea what it means and think if I understood the lingo better I will get the best usage from my new Harmony 1000. I have reviewed the user manual, but it is not as in depth as I would like.

Power Toggle - does that have to do with what happens when switching from one activity to another?

Discrete on/off?

Input? I think I know what that means, but I am not sure. Is that the source that say allows me to display my shows when watching my DVR,or the source that allows me to watch a DVD?

Other issues that I am not sure if I am the one causing the issue because of how I am using the remote or if it is the remote.

My activities
Watch DVR - devices: TV (Protron LCD) and DVR (from cable company), other devises off that are not in use. My issue with this activity is 95% of the time I do not mind that both the TV and the DVR shut off when I hit the power button on the remote. The other 5% of the time, I want to just turn off the TV and leave the DVR on. I thought I could get to this by setting up a Watch D-TV (downstairs TV) activity that is set to the same input to watch my DVR, but I do not think that is the way to go. Right now after turning on the TV and DVR with Watch DVR, I go to devices, choose TV and click the Off option. Of course, I think that may then knock things out of sync, but I am not sure.

Watch U-TV (upstairs TV - I do not have extender)
Issue 1 - I am not if it is because I do things like turn on and watch my upstairs TV and then go downstairs and do the above that I might be causing this issue. Say I have the U-TV activity going, go downstairs and activate the Watch DVR activity, then choose TV (the D-TV) device to turn off the TV, come back upstairs, click the activity button to see the available activities to choose U-TV this turns off the TV.

Issue 2 - Turned off TV with OFF button and the remote seems to reboot when place on charger. Two things happen - 1) the remote says it thinks everything is off - which is not always true b/c I may still have the DVR on 2) when I choose the U-TV activity there is a delay in the TV turning on and then a delay in changing the channel, but after that intial delay the delay goes away.

Toggle - one button that performs a different function each time it's pressed.
Power Toggle - one button that turns a device on, then off, then on, etc.
Discrete - one button (or command) that always does the same thing.
Discrete on/off - two buttons (On and Off). ON always turns the device on and if it's already on does nothing. Same for OFF. Discretes allow you to resend the command multiple times with no consequences. Toggles can only be sent once.

Input - for TVs and A/V receivers mostly, these are the various sources that you can switch to. A TV usually has different inputs for different connection types (S video, DVI, HDMI, component, composite). An A/V receiver usually has different inputs for different components (TV, DBS, DVD, Tuner, Aux, etc.). You have to set up each device so the harmony knows which inputs are available and how to select each one. Then you tell each activity which input to use for each device and the harmony will automatically select the correct input when you go to that activity.

I think the easiest solution to your problem is to simply leave the DVR on all the time. Most DVRs are designed that way anyway. Then you can hit OFF upstairs which will turn off the TV but leave the DVR on, then go downstairs and select watch TV again which will turn on the TV downstairs.

I do set it to always leave the DVR on?

The input selects and the rest of the commands should be in the database so you shouldn't have to enter this stuff. In the odd event that you have equipment that has never been seen by any Harmony remote then you have to learn to teach commands (with with Learn or Raw, which you can learn about - I had to do this for my TV - it was a Harmony virgin - a rare bird). With each activity you are completely in it or completely out of it. You can't interrupt with commands from other sources. Think through the logic - draw diagrams of what you want to do and how if you didn't have the Harmony. And then have it do exactly what you do. You can create as many activities as are necessary to achieve the result.