Uggh was just going through this process a few hours ago .. dealing with those horrible enter your cover letter and resume systems for X big company. I even just encountered this when applying for a job thru StackOverflow.
Overall those systems frustrate me to the point of finding the hiring managers name and their email address (just google for example @xcompany.com to see how their work email address is formatted) and sending them a personal message with my resume attached. This works at times, while other times it doesnt. But, either way I dont have to deal with those horrible CV/resume data entry systems. Also, since not many are using this hack Im sure the recruiting manager saw my resume vs. it going into a black hole.