Did you know that chipKIT boards can also be used as generic embedded controllers? chipKIT-compatible boards can be programmed not only with MPIDE or UECIDE, but also in several other IDEs using programming languages such C, C++, Pascal or Basic. When using another IDE such as MPLAB X, the chipKIT bootloader may become erased or over-written, which is fine, if you plan to stick with that environment. However, if you want to use MPIDE or UECIDE again after your bootloader has been erased, you'll need to restore the chipKIT bootloader. To do so, you can follow the Restore Your chipKIT Bootloader Guide with step-by-step instructions and lots of pictures. Knowing how to do this might save you from a massive headache ;)
Good luck!