*Correction: As noted by another user, Win+Page Up and Page Down can be used to change the monitor on which the Start screen appears. Apologies for any confusion - I forgot about this hotkey.
For the Start screen - it opens on the monitor you last did something in "metro" on. For example, if you opened the Charms bar (Win+C or hot corner), and open "Settings," Start will now open on that monitor. You can always force the Start screen to open on your monitor of choice by opening the Charms bar on that monitor and clicking on "Start" or by using the lower left hot corner. However, there's no way (to my knowledge) of doing this with the Windows key alone.
For the taskbar issue, you can change that. Right-click on the taskbar, choose "Properties." Under "Show taskbar buttons on:" select another option. I personally prefer "Main taskbar and taskbar where window is open." But to each his own.
I really like the app so far! Great work! I did find a couple bugs though:
1) You probably shouldn't use the same bar to split the article and comments that Windows uses to resize pinned applications. This makes it look resizable when it's not.
2) Sometimes my mouse's scroll wheel stops scrolling. I think this has something to do with the ad reloading. I don't know if you have any control over that, but I found it annoying. I think the ad is stealing focus.
3) The ad on the main page stays on top of the Settings flyout (Win+I -> Settings)
4) Right-clicking on the article side (the web control) causes the appbar to fly in and then immediately disappear. The article also flickers. This does not repro when right-clicking on the comment side.
Most of these are ad related, so maybe that's my cue to buy it... Otherwise, great app! I like it.