Thanks for your tips.
To clarify, are ISP programmers for bootloading and USB-TTL FTDI adapters for programming typically the same device or not? I tend to use a Linux OS rather than windows, so would my situation be the same when you mention drivers attempting to brick FTDI devices? Often I also run the arduino IDE on a raspberry pi too as well as using a normal x86 linux PC, just because a Pi can be easier to carry around when necessary. When using such device(s?) do I just run the arduino IDE as normal and use it for programming as normal, except that a specialised little USB will be used for bootloading or programming the ATMEGA chip, or must other settings changes be made?