I've been using the 5V 3A port at first, would charge really fast, but noticed that the battery would not last as usual. After switching to the 5V 1A, now the battery life seems more 'normal'. Given the year the laptop has been used.
Do you mean that if you charge up the computer to 100% using the 1A port the computer thens runs for longer than if you charge up the computer to 100% with the 3A port?
When it comes to these kind of issues I have learned the hard way to be sceptical of subjective impressions and only rely on hard data which can be difficult to obtain in a controlled way.
I would use the 5V 3A port personally. That is still only 15W compared to the 29W charger Apple supplies with the MacBook.