Red Bass line

Well, yes, as mentioned, you changed the instrument to flute, so of course the notes in the bass clef are red. Did you intend those notes to be be played by flute? if not, you should change the instrument to something else - ideally, one that is capable of playing those notes, as well as the notes shown in the top staff of that second instrument. Really, piano, organ, and similar instruments are the only instrument likely to be capable of playing that part.

To be clear, you have three staves, but only two instruments. The top instrument has one staff, and you've set it to guitar. The bottom instrument has two staves, and you've set it to be flute. If you intended those two staves to be two different instruments, you would need to add another instrument and copy the current contents of that top staff to it.