A back-up settings file should always retain the state that the settings were in when it was stored. If you upload a settings file and the values are not showing what they were when you saved the file, I suspect there were changes that were not applied yet when you tried to save the settings. I recommend always making sure the settings are applied (using the “Apply Settings” button) before saving your settings file.
Merging 3 sequences into one script that all play at the same time is not going to be very trivial, as there is no built-in support for merging sequences. Since the scripts are all generated with non-blocking delay functions, it will likely be difficult to manually merge them in a script unless you are very familiar with the Maestro scripting language and even then it might be tedious and somewhat error-prone, depending on your particular sequences.
Unfortunately, if you are not very comfortable with the Maestro scripting language, the easiest way to “merge” 3 sequences into one is probably to create a new sequence and go through creating each frame one at a time. A more advanced way would be to “merge” your sequences into one using a speadsheet program. For example, you can select all of your frames from each sequence one at a time by Shift+Clicking, copy them with Ctrl+C, then paste them to your spreadsheet program with Ctrl+V. You will see that each frame is a row, starting with the frame’s name and duration as the first two columns, followed by the servo positions for each channel. You can “merge” your 3 tables into one, following the same format, then copy the table with Ctrl+C and paste it into a new sequence in the Sequence tab with Ctrl+V. I definitely recommend making a back-up of your settings file before doing this, just in case you need to restore to a previous state.