I'll make up some examples of how the numbers play out, using the Street Samurai (SR4A, 110) as our test dummy.
This sammy has Body 4, Agility 5, Strength 5. She has two obvious custom cyberarms (each built with B4/A5/S5), both with Armor 2, Enhanced Agility 3, Enhanced Strength 2.
On any tasks that use just her arms (say, shooting a gun, or hanging on to something), her Agility is 8 and Strength is 7. On something that doesn't involve arms at all (say, running), she uses her base stats: Agility 5, Strength 5. If she tries something that involves all her limbs (like climbing or lifting something), she uses the average: Agility would be ((8+8+5+5)/4) = 6.5, rounded down to 6. Strength would be ((7+7+5+5)/4) = 6.
In cases where it's not terribly obvious whether her legs are really important, I would say to opt in favor of the character -- for example, swordfighting should use every part of the body, but that would work against the character who didn't opt for full replacements, and make melee attacks inferior to gunplay for this sort of sammy.
If, later on, the sammy wanted to improve the enhancements in her left arm (the right arm's full), she could not buy more than 1 in Strength or 3 in Body without also getting a cybertorso (required to get an enhancement of +4 or more). If she did this, she could get up to 1 Agility, 2 Strength, or 4 Body. Any higher would put her over her augmented maximum of 9, which is one of those "no you can't" areas.
Hope this clears everything up.
Situations can also change this. Hauling something off the floor would obviously use all the limbs (even if you lift with your back, your legs still need to support the weight) would call on the average; lifting up a teammate who's dangling off the side of a cliff (where the sammy is lying down, holding the poor schlub with one hand) would just involve the arm in question.
Two cyberlimbs would add 2 boxes to her Physical Condition Monitor (Stun would be unaffected). The limbs' 2 points of armor would stack with any worn armor, giving her 4/4 armor by default. With an armor vest (6/4), her armor would be 10/8.