I am trying to upload the complete software package to the project I am working on. Can I just import all of my C files into MCUXpresso (or some other IDE) and then directly upload all of the code to the OBC via the JTAG port?
What do your actually mean "upload" here? You want to integrate all you SW package into project?
For MCUXpresso IDE, you can refer to below two blogs (It is in chinese)
MCUXpresso IDE下添加新路径下源文件进工程编译的方法
MCUXpresso IDE下添加C++源文件进SDK工程编译的方法