Hi, welcome to the forum!
Yes, you can have files from any location as part of the same library and it shouldn't cause problems. Just beware of any settings that would move files (such as auto-organize), if you want them all to stay where they are.
If the external drive is disconnected, MusicBee will still show the files as part of the library but may ask to remove them or the display may change if it tries to rescan them. Don't mess with them, and the next time the drive is connected they should go back to normal (but take care that it always uses the same drive letter).