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I can't figure out how to set the ingame resolution to better fit the window size. Keyclone had this feature, but I can't seem to find out how to use this in ISBoxer.
I assume by "better fit" you mean "match the resolution to the region size". To do this, disable Instant Swapping in your Window Layout. (this will also bump your FPS up, see http://isboxer.com/wiki/WoW:Quick_St...considerations) You'll lose perfect mouse broadcasting by doing this, although you can apply a scaling option in your Repeater Profile.
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Another thing I'm tryin to figure, or remember, is how to take my saved settings for my main's addons and copy them over to my slaves. Particularly Bartender4 layouts and my Move Anything addon settings.
Each Addon is different, and has its own saved variable files in your WTF\Account folders. There is no good answer to this question unfortunately, I recommend setting them all up at the same time with broadcasting (Repeater), when possible.
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Another thing, I used to have my accounts set up with Symbolic linked folders with KC, is this still advisable for ISB or even needed? If not, come patch days, how do I update my slave's accounts?
No and no. You can use a single folder with ISBoxer. This is covered in http://isboxer.com/wiki/WoW:Quick_St...le_WoW_folders.
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I opened up the Task manager and saw that the .exes are running around 500k+ each on my system. Before, my main used to only take up about that much, if not less, and slaves only took up half that at all times. I've added more addons since then, but slaves have way less addons turned on than my main and all video/sound settings turned down to minimum and off, where main is the same, except for a couple things that's needed.
500mb per window is expected, I think this has been the case since wotlk.