I'm very new to embedded systems, having been on the Arduino bandwagon for a while I am now finally getting my feet wet at the chip level. While reading Elliot Williams' "AVR Programming" book (among other resources) I'm methodically setting up my toolchain. I purchased SparkFun's AVR Pocket Programmer and it works great with AVRDUDE. I have been able to configure it to program a chip from both Windows and 'nix environments, it's a pretty great tool. But I am interested in following in the footsteps of those of you who do this for a living, that is, I would like to use the tools that are the standard in this community. With that said, I went and downloaded Atmel Studio and configured it to use the AVR Pocket Programmer through and External Tool, but it "feels" clunky as it just runs AVRDUDE after a build. It seems that using this programmer removes a bunch of capabilities that I may be interested in, for example, reading the fuses on the chip from the Device Programming windows (ctrl-shft-p)). So, two questions:
1) Are there other important things I can't do with Atmel Studio 7 in conjunction of a non-supported AVR programmer?
2) What programmer does the community use for professional work? Are there any that are affordable? Say, < $100?
Thanks for the help