i guess i answered it in my head, but avoided actually answering the question...yes they are screwed down, and the "thin piece" it is screwed to is pretty stirdy being the whole width, and held down by the boxes which are wedged firmly up against the top of the trunk + the weight of the amps themselves etc.
The only reason i asked if it 'looks professional' is because to me it looks hideous, and i know it doesnt really look professional, but i want it to look acceptable, and to everybody i asked it is.
i do plan on figuring out where the little bit of noise is coming from and while im doing that, removing all the excess wire, and neatening it up.
ignoring the first part of your post, which is false in 90% of the population's ears, i do plan on lowering my next car, not this one because i do plan on removing all of the stuff i put into it, and selling it eventually.
the way the sub boxes are now is the perfect depth, height, and ease of access to easily remove them, yet keep them secure. The seat folds down with a quick release for the wires for easy just in case removal. this means i do have a trunk if i need it. The biggest problem with running the amps behind the sub's is the negative wire for them is too short, barely reaches as it is...this may seem minor, but i dont want to buy 8 gauge wire and solder that monster together...
i have had no need to fill up my trunk, and i dont plan on it. im not carrying logs, the most i have had to carry is my gym bag which can fit literally anywhere.
it is screwed down, and quite sturdy; an accident will surely jumble something up back there, but doesnt an accident jumble everything up a little? thats theh least of my concerns...
most of your questions were answered above, and what else do i use other than zip ties? honestly...the way the amps are i have no choice on which way the wires run; i guess i could try to just trim the slightly long pieces, but that is not going to make it look like a picture.
the boxes are just resting in there, but they are VERY snug, least of my concerns. there is one piece visible that is looped.
like i said above, i am not done with this, one of my RCA's is running too close to another wire (alternator charge to battery i believe) causing a slight whine which i have to take care of..while i do that i will try to neaten up a little better.