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Right Hand Technique

Until about 5 minutes ago, I used to place my right hand between the end of the neck and the pickup, until I thought "Hey, what If I rest my thumb on the pickup and play between the two?" I tried it, and it works. Is this bad? Should I have played like this before? Thoughts, tips, please?
 
It really isn't bad where you play at all. Playing closer to the neck gives a deeper, rounder sound (more like an upright bass), but the strings have a lot lower tension there so you have to be weary of fret-buzzing, playing over the pick-ups usually gives a pretty crisp sound (depending on the bass of course), and playing near the bridge gives a brighter and punchier sound, and the string tension is heavier so it may be easier to play quicker back there without fret-buzzing. A lot of players may go from one location to another in the middle of songs.

The only thing I'd be concerned about is getting comfortable with your thumb on your pick-up. It may limit your movements and/or slow you down. I personally like the floating thumb technique, where I lean my thumb against the lower strings to mute them as I play, and when I'm on my lowest string (an E because I play a 4 string), I leave my thumb floating there as if it was leaning against a string above. I just slide my hand and thumb up and down as I transition from string to string.

EDIT: And I just re-read your post and it seems like you may contorting your hand to play in between the neck and the pick-up while the thumb's on the pick-up. This could cause wrist problems. The first concern in right hand technique is to keep your wrist straight, no sharp angles. You should practically let you hand dangle in front of the strings, your hands should be very relaxed, and not forced into any position of any sort
 
As long as your wrist and hand are relaxed and comfortable, there's no "wrong" place to play with your right hand. Moving around in the area between the neck and bridge (and even over the neck) will open up a world of tonal options to you.
 
It's good to be accustomed to playing in several different spots. Move your right hand around to experiment, you'll find that you have a wide range of tones available to you, depending on where you pluck, and how you pluck.
 
If you keep your wrist straight after awhile it almost feels like your plucking a harp, particularly if you go lighter on your string diameter. I do my best to relax my RT hand as much as possible in finger style so that I can get more control & eventually work to using all four fingers. Personally, I don't always have to use a thumb rest position but when I do, I don't JAM my thumb down onto a pup or other rest; I just position it there to maintain a cleaner bridge position. The more I've been playing the more I relax & the more I relax - the less I look at the Bass & the more I listen. It pays off for me.
 
I tend to anchor my thumb on the E string on a 4, and lift off onto a P/up, or not, when the E is being played. Using the E as an anchor mutes the E string when your not playing it, and your not necessarily stuck around the p/up's for an anchor point, it allow's you to play at whatever point along the string. Its a matter of automating it so you lift the thumb when you play the notes in the line/piece on the E and re-anchoring. If I'm playing something that's predominantly played on the A D and G strings I think about anchoring on the A, keeping that and the E string muted, a bit like floating thumb technique. My 2.