Those are some pretty vague questions.  

  Most of them cannot be answered unless you tell us what online stores you're considering to buy from.  Not all online stores offer bundles.
Try going to the store in question, putting the motherboard, CPU and heatsink in the basket, and going far enough into the checkout process to determine what the shipping cost is.  Then empty the cart and do the same with the equivalent motherboard/CPU/heatsink bundle, if they offer bundles at all.  
It sounds like you are new to the online computer-store scene, so may I recommend looking for companies with good ratings at 
www.resellerratings.com and/or 
http://www.anandtech.com/ratings/index.html to help you determine if they're a good store or not.  You should look for stores that have good ratings based on large numbers of feedbacks, not just a few feedbacks that might have been put there by the employees.
As far as reliability, my guess is that more systems fail to work due to user error than due to faulty parts.  For instance, putting the heatsink on the CPU backwards, or installing the motherboard so it is grounding out where it shouldn't, are a couple of things which are beyond the control of the store.  Still, if the part is genuinely faulty, you don't want to be left holding the bag.  So pay attention to those ratings.  
