Myriad will only drop 'songs' not adverts and links (jingles and promos etc.).
If you have a long 'manual' sequence of shows, lets say starting at 1pm the presenter stops automation, then several hours later, say 6pm, the presenter starts automation, but with the log still at 1pm, the system will need to do some serious 'dropping' of songs to get back on track - so you end up with a long series of no songs, just back to back jingles and promos and adverts, if there is enough of these the system will still over run 6pm.
Dave Boulton's command suggestion seems a good one - from memory I think you can script jumping to the 'previous' and 'next' hours in the log - I'd add this into the mix to ensure you started from the start of the log hour, not some items in if the presenter starts automation late.
Another option is to schedule 'empty' hours when you know there will be a live programme, and just let automation sit there waiting for each hour to finish, the presenter can still play carts manually - and then the system will just kick in at the apporiate time.
A variation will be stick a single jingle at the start of the first 'live' show, set the log to 'live' mode and put a 'stop' at the end of this item, then the presenter can just press 'Q-Nxt / log Go' at the end of the live sequence. The down side to this being if for any reason the presenter doesn't turn up the system just stops.
Myriad user since 1998, now custodian of dozens of Myriad,Autotrack, Powerlog and Scoop boxes of many different flavours.