Ok (iFuntastic) if you have a bunch of icon.png's then you go to the specific application like SMS ans then open that up, find the icon.png in there on the left hand side is a little blue box you can click on, choose replace and find your new icon. do this for each application you want to change. OR if you have the whole application in an application folder (a lot of the themes are like this now) then you can just drag and drop OR do the process above
this will completly change your home screen you wont have the old icon sets anymore. I installed summer board and have been messing around with that, changes wallpaper, and icons. there is a ton to choose from now as well. I am trying my hand at my own summerboard theme but I dont have photoshop so it is kind hard creating. but I am learning. I also started to use Openssh on most things. it is a little easier now that I have learned a little about it. (plus you can always restore!!

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One word of advise: I dont use the homescreen tab in iFun it puts a black box around all the icons, if you want to move icons around download rSBT from installer works GREAT!! you can even hide icons you dont want (I hid stocks)
Ifun: method one above, go to file manager, then in the second area click the drop down arrow in the very top box and go to the desired application, look for icon.png and replace.
method two: file manager/home (click the home button)/applications
Good luck and let me know how it works for you.