I would think that the music is paused with the scene, but if it doesn’t work, as you said, you’ll have to save the offset manually 
There is an expression to get the music playing offset, and an action to set the offset too. When you pause the scene A and go to scene B you can save the music offset in a variable on scene A, as it’s a scene variable it’ll be saved in A because A is paused. Then you go to B, when you return to A you can set the music playing offset = the saved variable.
A numeric variable is 0 by default, so the first time you load the scene A the offset will be 0, and the music will play from the beginning, no problem here:
[code]Conditions: At the beginning of the scene
Actions: Play the music on channel 0
Set the playing music offset = Variable(music_offset)
Conditions: Conditions to go to B
Actions: Do = MusicChannelPlayingOffset(0) to the variable “music_offset”
Pause this scene and go to scene “B”[/code]
Not sure if the “At the beginning of the scene” is launched again if the scene has been unpaused, if it isn’t launched you’ll have to add a variable that works every time the scene is unpaused:
[code]Conditions: Variable “unpaused” is = 1
Actions: Play the music on channel 0
Set the playing music offset = Variable(music_offset)
Do = 0 to the variable “unpaused”
Conditions: Conditions to go to B
Actions: Do = MusicChannelPlayingOffset(0) to the variable “music_offset”
Do = 1 to the variable “unpaused”
Pause this scene and go to scene “B”[/code]