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If the replacement head unit fits neatly in the existing slot without any bodging you should be able to replace the original afterwards.
It is possible to buy ISO adaptors which fit on the new unit so you can retain column controls.
When it comes to sub amps etc it would be necessary to have adequate fused power cables and earths installed. Poor installations can result in overheating and even fires. I suggest you inform your insurers of any changes you make.
For head unit adpators you could try the link below for information
P.S. - when it comes to in-car audio I ain't no expert as boom boxes do absolutely nothing for me but each to their own I suppose.
Currently in madnoel10's garage:
Honda Civic 1.4l