What Happens when I use all of my CPU resources?
Short answer is that your PC or OS won't fail, it can perfectly well handle a situation like that. Probably all fans will run full speed to cool the system, but the system is designed for a situation like that.

Not CPU but memory should be your worry.

Only thing you want to watch is swap use which you don't want near 100%. If that happens you apparantly have too little RAM (and/or swap space) and Linux will start killing random processes to prevent the system from crashing. (Actually it does a slightly educated guess when selecting processes to kill and in this case your ffmpeg process would have high likeliness te be killed.

top - 11:53:33 up 5 days, 14:00,  3 users,  load average: 1.08, 0.84, 0.79
Tasks: 246 total,   2 running, 243 sleeping,   0 stopped,   1 zombie
%Cpu(s):  6.4 us,  1.5 sy,  0.0 ni, 91.3 id,  0.7 wa,  0.0 hi,  0.2 si,  0.0 st
KiB Mem:   8074916 total,  7511956 used,   562960 free,   476140 buffers
KiB Swap:  8388604 total,  1521824 used,  6866780 free,  1223412 cached
                                          ^^^^^^^^^^^^


In any case your system will not be physically damaged by high CPU or memory load.