I was wondering if there is a way to get rid of your old bots so they can be replaced by the new bots or do you just ditch them in a corner?

You can put bots into the Recycler to get back the parts used to build them, or you can put bots into the Incinerator to just get rid of them, but why would you want to replace them with new bots?  You could just retrain the old bots to do what you would otherwise make the new bots do.  You could even use the Crude Data Storage to retrain an old bot to do the same tasks as another bot if you want.

Thanks, I could.

In the next version you'll be able to replace individual body parts as you upgrade them, thereby avoiding having destroy the old ones and reprogram them. Much easier! Of course you still end up with left over body parts :/

Dont you just love to Frankenstein robots into pure awesomeness? 

The only problem I see with the Upgrading robots is the Lvl 1 bots. I get converting mark 2 to mark 3 and so on. But how would you do that with the first generation?