I've read several interviews by several pros that think the acoustic and amplified sound of your bass should be treated as different things.
You don't really have a choice; they are different things. I have found that the best plan is to learn how to work with the amplified sound to create the best possible sound to enable you to forget about the sound and put your attention on the music itself. It is all-to-common for us to get caught up in worrying about the wrong things. There are lots of great recordings where the sound of the bass itself might be less than ideal but the music transcends that. There are lots of examples of just the opposite. I am sure that Scott LaFaro wasn't thinking about how great his sound was on the Village Vanguard recordings... If you can think of your acoustic and amplified sounds as being separate (but hopefully related), getting a pleasant and workable amped sound should not be that hard, provided you can get a good acoustic sound and you have at least a decent amplification system.