#1
Here is my problem:

I have an American Deluxe Strat
I have a Fender Hotrod Deluxe tube amp

But for some reason, I'm not getting good sound. The hardware is all working properly.

I find that the best guitar setting, is to have my guitar on the treble pickup (the one that is the most trebly)

If I use the other three pickup setting, my sound is muffled.

I try to keep things simple by just using the footswitch that came with the amp, and sometimes a Boss chorus pedal, but how do I go about getting a better balanced sound? 

Any advice?

Thank-you. I am miffed because I've seen people with all kinds of setups (more expensive than mine, and also cheaper than mine) with much better sound. 
#2
If your sound is muffled with the neck/middle pickups, you need to turn up your tone knobs/turn up the treble and presence on your amp. They are not dark pickup positions, but rather introduce more bass and low-mids. In contrast, the bridge pickup (what you call the treble pickup) cuts bass and low mids.

Start with the amp with flat EQ, and go from there. Try not to make extreme EQ adjustments, do not scoop (heavily reduce) the midrange. The HRD's natural drive is often not liked by many players, using an overdrive pedal on the clean channel, or with the preamp gain low on the lead channel, will likely get you better results for drive sounds. That also said, if you're trying to get metal out of a HRD you have the wrong amp. Blues and Classic Rock fit the HRD's resume.

If you have had the HRD for a while, you might want to change the tubes as well.
#3
Will Lane Will

I found your advice very helpful Thank-you. I will try what you suggested. In terms of my use ofd the amp, I'm a classic rock guy, so it should work. But I was not aware of the tips you provided.

Thanks again!
#4
Can I ask you to explain this more:

or with the preamp gain low on the lead channel, will likely get you better results for drive sounds. 

Are you saying that having the preamp gain low, gets a better distorted sound? If so, can you explain why? I just like to udnerstand how it works. 
#5
Quote by Music Fusion
Can I ask you to explain this more:

or with the preamp gain low on the lead channel, will likely get you better results for drive sounds. 

Are you saying that having the preamp gain low, gets a better distorted sound? If so, can you explain why? I just like to udnerstand how it works. 
Sorry, I meant to suggest that you keep the preamp gain low on the lead channel but you also use an overdrive/distortion pedal to get the distortion levels you need.