Not sure if they can run together but don't see why they couldn't I guess. As far as setting it up it progressed to that for me. I'm not very good with scripting and code honestly. So I did things by trial and error. I'm sure there's a better way to write the script than I did. Probably the hardest part is finding the coordinates for where you want to click. That wasn't to bad though just take a screen shot and find out your x and y's are and use those. So for example.
Code:
<Hotkey LButton>
//------------------------------------------------------
// Bore
// /cast [mod:LCtrl,target=Bore] lesser healing wave
// /cast [mod:LShift,target=Bore] healing wave
// /cast [mod:LAlt,target=Bore] Riptide
// /cast [target=Bore] Chain Heal
//------------------------------------------------------
// Top half of unit frame
//------------------------------------------------------
<If MouseIsOverWindowRect WoW1 768 1049 74 68>
<SendLabel w2>
<Key LShift G>
<Else If MouseIsOverWindowRect WoW2 768 1049 74 68>
<SendLabel w2>
<Key LShift G>
<Else If MouseIsOverWindowRect WoW3 768 1049 74 68>
<SendLabel w2>
<Key LShift G>
<Else If MouseIsOverWindowRect WoW4 768 1049 74 68>
<SendLabel w2>
<Key LShift G>
<Else If MouseIsOverWindowRect WoW5 768 1049 74 68>
<SendLabel w2>
<Key LShift G>
//------------------------------------------------------
// Bottom half of unit frame
//------------------------------------------------------
<Else If MouseIsOverWindowRect WoW1 768 1134 74 66>
<SendLabel w2>
<Key G>
<Else If MouseIsOverWindowRect WoW2 768 1134 74 66>
<SendLabel w2>
<Key G>
<Else If MouseIsOverWindowRect WoW3 768 1134 74 66>
<SendLabel w2>
<Key G>
<Else If MouseIsOverWindowRect WoW4 768 1134 74 66>
<SendLabel w2>
<Key G>
<Else If MouseIsOverWindowRect WoW5 768 1134 74 66>
<SendLabel w2>
<Key G>
That's a snippet of my click healing script. The above is for when I left click my pally unit frame. The WoW1 is what window I am clicking. The 768 1049 is where the imaginary square starts in the upper left corner of the square. The 74 68 is the size of the square. The sendlabel is what window you want the key to press in. In this case my healer is w2. Last is the actual key you want it to send. <Key G> is the key being sent. You can also have it actually mouse click on a area on one of the window's but I wasn't sure how reliable that would be but you could do that to use something like clique or healbot. I have a piece of that script for each character and for each click left, right, and middle. You could also use mouse 4 and 5 i believe but i use those for something else. I know it looks daunting if you are new to this kind of stuff but it wasn't nearly as tough as I thought it was going to be writing the script. That is once you get the hang of it anyway 
Plus there's lots of info here and on the hotkeynet forums to help ya out. Not to mention Freddie is pretty good with helping. Love these forums for support!
EDIT: Almost forgot if you do try using something like my script you will want the mouse to act normal when not clicking in those area's so you would add this code at the end.
Code:
<Else> //--Defaults mouse to normal when you dont click a predetermined cordinate
<SendFocusWin>
<ClickMouse Down %Trigger%> //--Use to allow mouse look with left click
<HotkeyUp LButton> //--Use to release left click when mouse looking
<SendFocusWin>
<ClickMouse Up %Trigger%>
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