> I understand that there is no way to make crossarchitectural application (so it runs on x32 and x64 architectures without any changes).
> I have to do different assemblies due to the fact that x64 fbembed.dll not be used as x32 or x32 fbembed.dll not be used with x64 JayBird.
> And, of course, I can not get x64 JayBird to work with x32 fbembed.dll.

The main issue is neither the Jaybird nor Firebird - it is JVM.

If you use 64-bit JVM, you must use 64-bit jaybird22_x64.dll and in turn
you must use 64-bit Firebird Embedded.

If you use 32-bit JVM, you must use 32-bit jaybird22.dll and 32-bit
Firebird Embedded.

You can run 32-bit JVM on 32-bit and on 64-bit platforms (Windows,
Linux), but you are limited to 1.5 GB heap. If you need more heap, you
have to use 64-bit JVM and in turn only 64-bit Windows or Linux.

So, decide first if you can live with 1.5 GB heap, if yes - stick to
32-bit JVM and then you have less troubles with different assemblies.

Roman