The simple answer is "it depends"...
For the rear part of the Amp, I modelled all the individual items in their own layer(s), and then transferred them via copy/paste into the same layer as the amp chassis itself. However, things like the power selector may (or may not) be transferred back into their own layer at a later date (all the control switches on the front for instance are in their own layers so I can animate the amp being switched on).
The rear of the Cab, has the main rear panel being modelled as a simple bevelled box (whereas the outer shell of the cab is a subpatch object). The speaker patch bay was again, modelled in its own layer, and eventually transferred to the same layer as the main cab.
The simplest way to look at it is if the item might need modification or animation, then leave it in its own layer, if not, then bring it in with its related parts to ease headaches in layout.
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