One device clock master, the other clock slave.
Whether you use Word Clock or one of the digital ports for clock synchronization is up to you.
The DAW can access both devices via the same ASIO driver.
Ensure that both devices use the same ASIO buffer size.

I wrote you already that it depends on your choice.
I can not tell you an optimal route for driving to XYZ, if you do not tell me if XYZ is the airport or a railway station.

You can clock via
- Word Clock
- AES
- ADAT1
- ADAT2
- MADI optical
- MADI coax

You must proceed on the principle of exclusion. If you don't want to use or reserve a particular digital port for any other purpose, and if the digital port is not connected to a device other than the 2nd UFX+, it would be available for clocking.

I would exclude / reserve i.e. ADAT2 because this is the only optical ADAT port supporting ADAT and SPDIF protocol.
If you might need to connect coaxial MADI devices, then you can't use the BNC connectors for Word Clock.

I would assume, that your two UFX+ devices are not connected to the same MADI bus, because this might have an impact on the automatic delay compensation feature depending on where in the MADI bus "chain/ring" you place the 2nd UFX+. So lets simply assume you would use two MADI busses separately as this also enables you to have two separate MADI channels (2x64 channels more). So we exclude MADI here for clock sync between the two UFX+. Of course you can use MADI for clock synching MADI devices like i.e. Octamic XTC that are connected to a particular MADI bus.

AES and ADAT2 port are bridged, see block diagram, so I would leave this out as well to make things not to complicated.

Another point, how is the distance of the two UFX+ to each other ? ADAT TOSLINK cable can be up to 15m maybe even 20m, but this is already outside of the usual standards if I remember right. WC cabling can be longer.

This you need to consider to draw a good decision.

Lets further assume (to come forward in the decision making process...)
- you do not need to clock sync even more devices to each other, thus that you have no master clock for WC
- the two UFX+ devices are close to each other, under 15m, maybe even in the same rack one underneath the other
- that a connection between both devices using ADAT1 "does not hurt"

Then simply buy this cable at a length of YOUR choice between 0,5 and 15m, I would choose 1m for more flexibiltiy:
https://www.thomann.de/de/mutec_optisches_kabel_1m.htm

Plug it between UFX+ #1 (Clock Master) ADAT1 OUT and UFX+ #2 (Clock Slave) ADAT 1 IN.
In the RME driver settings dialog set
UFX #1 to Clock Source "internal" (master)
UFX #2 to Clock source "ADAT1" (slave to clock signals read on ADAT1 IN port)

In the TAB "About" you can "determine" / "fixate" the sort order for all devices that are supported by the MADIface driver,
so for the two UFX+ and also other devices which could be added like ADI-2 Pro FS R BE, etc ...

> Regarding the settings of the clock source, the only way to set the second soundcard is to plug it to the computer.
> Indeed otherwise in the panel "Fireface USB Settings" I can see only one interface.

Of course.

> However, doing this causes my audio programs (e.g. Pure Data) to see both soundcards

Yep.

> and I am forced to select one of the two.

Select ? Nope. You have two equal interfaces and your DAW is able to access both recording interfaces.
I also have two UFX+ and Cubase is able to access all channels of both interfaces.

> Instead, I need to control from one single program both soundcards (in particular the analog
> output channels 1-8 from the first soundcard and channels 9-16 from the second)

What do you mean by "One single program" ? The DAW or TotalMix FX ?

Fact is ...
- connect both interfaces via USB
- clock synch them as described
- make always sure that both interfaces are set to the same ASIO buffer size
- DAW can access all channels of both devices directly via MADIface ASIO driver
- You have two different TM FX instances, one for the primary, one for the secondary UFX+
- You can open one TM FX window per UFX+ instance or make all in one window, by selecting the unit you wanna work with
- On TotalMix FX level you can only perform any to any routing inside of one UFX+ device
- If you need to route channels across the two UFX+ devices, then you need to perform this in the DAW

You could have mentioned that already in your first post. And save Ramses and all readers a lot of time.

TM FX is very flexible and allows you to switch between two interfaces, or open multiple windows instead. Described in the manual, although all one needs to do is check the available menu entries in TM FX...

The manual...Using multiple interfaces is described in the respective Mac chapter, function Aggregate Devices.

> It's hard to believe that you could even think of mentioning it in this century. Great sausage.

I don't really get what you mean...  sarcasm? Not really funny.

Thanks to the administrator for the tip of checking the manual, which I will do shortly.

Is it that fundamental to use Windows for the problem at hand? I have been using RME products for 15 years, both on windows and mac. And to be hionest almost 10 years ago I was connecting without problems 2 firefaces 800 via a firewire cable, using a mac. Now, the question is: can I use the 2 UFX+ connected and using a Mac? My understanding is yes, although today I could not solve the issue. Not sure however what mac-specific driver I should use, if any (?).
Tomorrow I will read the manual, but reading at the posts on this thread it is not yet clear to me what one using a mac has to do. I followed the steps. And I don't have Asio drivers, not clear why they are so important.As far as this matter is concerned, RME should be working on both Mac and Windows. Right?