Homebrew PCBs

hi guys,
I am new to this group. 
I checked the archives and found some interesting things, but nothing about
home-brew through plating (or DIY equivalent).

How do you guys manage the double sided assembly? not all components allow
soldering on both the solder and component side (caps, DIP bases, connectors,
etc). Also there is the problem of vias under SMDs and the CAD packages (I use
mainly EAGLE) are not very helpful/happy in placing 'redundant' vias for
'wired' through-board connections.


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