Pickit 2 with the ATMega

Right, then we have to get the terminology right. Will these barebones boards have a bootloader on them? If not, the FTDI interface won't put it there. You need an ICSP programmer (one that uses the SPI interface) and I strongly doubt that the Pic Kit will do that. Its interface will be for PIC chips.

To save costs, if you have at least one Arduino already you can use that as an ICSP programmer. Search for "Arduino as ISP". I wrote a sketch that lets you put code onto SD cards and program bare baords, as described here:

Example in use:

However you can get cheap ISP programmers. eg. This one for $20: