I have only made one bag from a pattern that was for a friend and since then I have made up my own patterns (currently using a bag I made a few weeks ago: please see photo below)
I ALWAYS use 1/2 inch seam allowance as I would rather be safe than sorry. As for lining this up on the machine: my sewing machine has 'groves' on the plate and I measure from the needle out to the required seam allowance and mark it with a pencil line. Works for me everytime.
Don't be discourage with your errors - you will learn from them and your work will get and be better. If in any doubt do a toile/dummy run first so that you don't spoil the fabric you actually want to use. You may think this is a waste of time because you are making the same item twice but if you make errors on the toile you can make notes so you don't do it on the actual fabric. Use different colour fabrics and threads so you can see your work clearly and any errors you make. I write on post it/sticky notes and staple them to the required area so that they can't come off. Use this bag as a template of the finished design - you will learn a lot by doing this and your confidence in sewing will grow without you realising it.
Glasgow, Scotland, UK (Monday 1 October 2007; 22:18BST)