ISBoxer can't override Action Bar bindings, and does not put macros on your Action Bars -- it is designed to only make temporary changes to WoW, so you can play without ISBoxer and not be inconvenienced by the changes it made. Sorry

The "fix" for this is to continue using 2 (for example) for your Hotkey (what you push), but change the Key Combination for the WoW Macro Action to something that ISBoxer can use. It can be as obscure as you want, most of mine are like ctrl+shift+alt+Q (something I'll never press)