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Simeon,
You mentioned Linux in the subject line, therefore I assume you are using this OS and would like to perform low-level debugging and code loading - i.e., skipping the OS as you mentioned.
In this case, the IDE will allow you to go through the process of creating the code in C/C++ or assembly, loading and/or inspecting the code loaded to the target and interact with its memory contents.
Answering your questions;
1) The best procedure to get acquainted with CCS is to follow the Getting Started Guide, which goes through the process of installing, creating the first project and debugging it.
2) Although the guide above uses the software simulator, this can be easily extended to the hardware. Choose the appropriate options in the section Creating a Target Configuration File shown in the chapter Project debugging. In the case of BeagleBone the settings are Connection: XDS100v2, Device/target can be either AM335x (the Generic) or, if you installed the device support files (link shown in the guide) you also have a BeagleBone device/target.
3) To write the code you must have a knowledge of assembly, C or C++. However, when interacting with Linux and its pre-bootloaders (xloader and u-boot) you will have to reference additional documentation for the software package (SDK) suitable for your board.
http://processors.wiki.ti.com/index.php/Sitara_Linux_Software_Developer%E2%80%99s_Guide
Other two references that will help you perform debugging in such environments are shown in the two links below:
http://processors.wiki.ti.com/index.php/Linux_Debug_in_CCSv5
http://processors.wiki.ti.com/index.php/U-boot_Debug_in_CCSv5
Regards,
Rafael