Okay guys, ease up a bit, will you? There is no need to be rude (in fact, there is NEVER a need to be rude, ever, even in response to someone else's rudeness).
First - this is NOT a rules question, clearly, and should be in House Rules. It looks to me like the rules are clearly understood.
Nonetheless:
As far as the change to the rules - what you propose makes a certain amount of sense, certainly. It's definately not the rules, though.
If this is one of the only exceptions you are making to the rules, go for it - it will be fine.
If this is one of many House Rules you use, don't do it. You are making the game over-complicated and unpredictable for your players. They need to be able to use the rules as written to plan their characters. Be very, very careful about introducing House Rules into your game. It can take predictability out of the rules, and that's a Bad Thing.
Finally, for your visualization problem, let's use a ranged touch attack with an electrical damage effect for an example:
1. No Sneak Attack: You fire your electric bolt out of your wand and hit the bad guy - the force runs right through his metal armor and underlying leather protection and zaps him for xxx damage.
2. Sneak Attack: You fire your electric bolt out of your wand and hit the bad guy - you managed to hit just the right spot on his helm, where it connects directly with his chain armor underneath, which, in turn, rests partially on his bare neck. The electric charge is sped along its way by your outstanding choice of target, and the bad guy takes xxx damage + xd6 more of sneak attack electrical damage.
How's that?