When I track my expenses I want to ignore them – as I set a budget to spend $1000 this month. Savings are not really an investment but if I transfer $500 into savings it's hard to track the budget – maybe some reference code could help with that.
There has just been a project submitted to solve this on HN – https://blog.teller.io/2017/06/12/the-api-for-your-bank-acco...
But it seems to support only a handful of UK banks – no ANZ or Kiwibank.
Once the money is in my savings account I do choose to reallocate the extra (beyond emergency fund) to long term investments.
It's also impossible to go over budget without noticing, you'd have to take the difference out of the savings account. If your budget is wrong you'll notice immediately.
That's just my approach though, and it works for me. Other people may have different methods that work for them.