Do I need to clear the bootloader when using Parallel Programmer?

I am in the process of building a parallel programmer, currently all of my chips have bootloaders on them, do I have to clear the bootloader in order for this method to work or can it still program and can the program still run with the bootloader in place.

If I have to delete the bootloader, how can I do that? I haven't been able to find anything on this, I think it may be possible to use an mkii and AVRStudio but I am not too familiar with those. I have access to an mkii but I want a parallel programmer so I have my own programming capability.

Usually you would use a parallel programmer just to load a fresh bootloader. When you burn a bootloader the chip is completely erased as part of the process.

If you want to get rid of the bootloader to make more space you won't be programming an Arduino anymore and any problems you encounter will be outside the scope of this forum. Perhaps you should visit where the people who do raw AVR programming hang out.