First, you (and/or your client) need to define just what "MANUAL MODE" means. See
THIS THREAD for some some of the problems.
If you decide that Manual means complete control (within safeties), then just combine the modes:
MANUAL MAN_START MAN_STOP SAFETY RUN
---+---| |---+----| |----+----|/|-----+----| |------( )
| | | |
| | RUN | |
| +----| |----+ |
| |
| AUTO AUTO_RUN |
+----| |--------| |----------------+
The AUTO_RUN bit is some output from your sequencer that tells the device to run.
The SAFETY bit is all the conditions that are required for the device not to cause injury to someone or something. This is not a substitute for hard-wired safeties, just a backup. (It also makes sure that when the hard-wared safeties are restored, that the device doesn't start up unexpectedly because the seal was still made)
Make sure that the sequence dosn't advance while a device is in Manual mode (unless you really, really want it to. If the sequence is doing several things at once, it can get lost quite easily in manual mode.
This sort of thing
must be designed from the first rung - it cannot be grafted onto a project at the end, or you will wind up with spagetti code.