@Anoeta0
On your calendar, there is a tool called 'rule sets' which you can use to prevent check ins on particular dates. However, you would need to go in and manually set this for every relevant date, e.g. as soon as you get a booking for one unit, go into the calendar for the other unit and add a rule set for that date.
I don't know of any automatic way you can do this, but perhaps there is one that other hosts know about.
I also do the check ins myself, but as my listings are in the same house, it's not normally a problem. I try to stagger guest arrivals, but if they arrive at the same time, it's not a disaster.