I will jog the z axis down to the work piece and zero it........................................................However on the sample programs, I see some positive numbers and when trying to execute - I get the soft limit warning.
When the top of your part is zero, there should be some positive distance from zero up to the top of your travel. Machines with longer Z axis' will have more positive travel.
Are you homing the machine at the top of travel? The softlimits are in machine coordinates, and if you don't home the Z at the top, then your machine zero may be below the top of travel, thus triggering the softlimits.
Never used the multipass, so can't help you there. But sometimes when entering cut depth, some programs accept positive numbers for depth of cut, even though the g-code will be negative numbers.