Linux is quite good at scheduling the CPU time of running programs: Even when a process is running which constantly uses up all processor power, it is still possible to use another (interactive) program nearly as fast as on an idle system. But if a process is doing heavy I/O operations (i.e. backup software), the response times of interactive programs can be heavily increased.
A possible solution for this problem is the command line tool ionice which can be used to control the I/O scheduler. For example, if a backup tool is to be run, running
ionice -c3 COMMAND
will execute COMMAND with the scheduling class “idle” (will only run when no other process needs I/O).
Have a look at the man page for more information.