Hi Harry,
Sure. I am glad to answer your questions.
1. Of course you can specify any config file you like with the -conf command-line option. For example, "dosbox-x -conf myconfig.txt" will specify "myconfig.txt" as your config file.
2. You can either specify a different directory just for the config file or a different working directory for DOSBox-X (and in such case the config file and so on will be loaded from this specified directory). For example: "dosbox-x -conf c:/dos/myconfig.txt" will load the config file c:/dos/myconfig.txt. Another example: "dosbox-x -defaultdir c:/test" will set c:/test as the DOSBox-X working directory, so that config file (and other things) will be loaded from this directory.
3. You can change many config options on the fly via the CONFIG command, e.g. "CONFIG -SET fullscreen=true". But you cannot load a completely different config file without restarting DOSBox-X.
4. Whatever appears in the text field will be saved as the config file. Clinking one of the three buttons (e.g. "Use primary config file?" simply changes the content of the text fileld automatically according to the button you clicked. When you click the "Save" button DOSBox-X will actually save the configuration to the config file as appears in the text filed.
5. Yes. The current configuration will be saved.
6. DOSBox-X has a lot of config options, but they either belong to "common" or "advanced" config options. If you don't click "save all config options" then only the common config options (and any modified advanced ones) will be saved to the config file. Compare the files dosbox-x.reference.conf and dosbox-x.refernece.full.conf to see the differences between a config file with common options and a config file with all config options. The former one is about 57KB and the latter one is about 194KB. You see the size difference between them.
7. DOSBox-X's Windows installer clearly offers the option to save all previous settings while upgrading, but I wonder which option did you select during installation? "Yes", "No", or "Cancel"? As described in the installer it is recommended to select "Yes" to automatically upgrade the config file while automatically keeping all previous settings. But did you select "No" instead? If you selected "No", then dosbox-x.conf will be reset to the default one and your previous config file will be renamed to "dosbox-x.conf.old" without changes. If you selected "Cancel", then your dosbox-x.conf will be kept as is without any changes or upgrading. The Windows installer will never kill your previous setting no matter which option you had chosen, but your setting will be kept in different ways according to which selection you had made.
Hope this helps.
Sincerely,
Wengier