Every Yaesu I've ever programmed could differentiate between repeater frequencies and simple frequencies automatically because the band plans are incorporated in the firmware. In other words, if a repeater frequency were entered, the radio would automatically apply the proper offset direction (+ or -) and amount of offset (600 KHz or 5 MHz on a dual band radio.) The tone and tone settings have to be entered separately.
For a simplex channel, all that's required is to enter the frequency when the radio is in VFO mode and then follow the steps required to write it to memory.
Looking at the FT4XR manual, it appears this radio is just the same. All you have to do is enter the simplex frequency—making SURE it is a designated simplex frequency according to the band plan—and then write it to memory. No change to the AUTOMATIC REPEATER SHIFT (ARS) menu setting is required!