To avoid the overloading with the official iota nodes, I have setup my own iota node. I then went ahead to do some transactions but while some are confirmed, most are pending. Is there any way or tool that I can used to get all the transactions that I'm doing on my node automatically confirmed?
The coordinator is the final decider whether a transaction is valid or not.
Therefore there's no "tool" that confirms transactions with a (near) 100% success rate.
What you could do is keeping track of all transactions you've sent (in a database for example) and check every few minutes if they are still pending. If so, promote them (this increases confirmation chances a lot) or reattach (if they are pending for >30 minutes). Usually promoting a few times will be enough for 90% of transactions.
PS: There are web apps like http://reattach.online/ available which automatically promote transactions if you give them the tx hash and leave the browser tap open