Hello,
well, if You are trying to program FPGA with Your own design, it may need its own DeviceTree file. It is need in case You add, remove or change some parts of design in comparation with GRSD such as e.g. peripherals of HPS IP core in QSys.
The other possible source of problem would be incorrect FPGA design. The serial link to processor has to be set in Qsys in HPS IP core in a very same way as in GRHD. The proper settings would differ according to Your board, however, so try to look at the page of Your board at RocketBoards. There You will find the right GRHD and the proper settings.
And to answer Yours second question - You can open session beside serial link also via ethernet. SSH protocol is used for this way. If You use PuTTY, You only need to switch ‘serial’ to ‘SSH’ and type IP address of Your board.
However, You will not be able to connect as ‘root’ user (with password verification), due to default security settings. If You would like to try it, You could find details here: https://forum.rocketboards.org/t/transfer-file-on-sd-card-from-windows-host/1520/5?u=jankonecny.
Best wishes.
Jan Konečný.