TL;DR: I have five main suggestions. They are in bold, below. The rest is mostly commentary.
The Presto system has some quirks. The system has also had problems in the past.
1. Set up Autoload using a credit card. If there are any system foul-ups, this may help to protect you.
If you have Autoload-related problems, phone Presto. If they don't help, phone your credit-card issuer.
If the Presto system attempts repeated unjustified Autoloads, as it has done to others, you won't be hit with $150 of NSF fees.
If you do use a debit card and have problems, the money will already be missing. You can phone Presto; you can phone your bank; you can contact the BBB; you can file an Ontario Ombudsman complaint against Metrolinx; or you can go to small-claims court. But these options might not help.
2. If you only have a debit card, it may be unwise to set up Autoload.
Debit-card Autoload and Period Pass Autorenew are convenient, but carry risks. (See above.) You can live without them.
3. It may be wisest to choose a threshold of $20 or more.
Autoloads are supposed to be processed instantly and automatically, with no 24-hour delay. Recent system changes have made it possible to choose a threshold of $5, but that doesn't mean you should. There are rare cases, including credit-card expiry, credit-card failure, and others, in which a $5 threshold Autoload can fail.
If you can afford to set a threshold of $20, consider doing so. If you use GO Transit daily, you may want to choose a threshold which is even higher.
4. Don't choose an Autoload amount over $50 unless you use GO Transit.
Presto refunds are a hassle. Refunds over $50 are a big hassle. Don't keep hundreds of dollars on your card unless you use GO Transit daily.
If you ever decide to stop using Presto: Use up most of the money on your card, then give it away to a trusted friend or relative.
5. Know that Autoload may not work correctly if your card starts out below the threshold.
If your card has $3 on it, and you set up Autoload, the card may or may not reload itself. If Autoload fails to work, your card may eventually end up in overdraft, and you may need to schlep to a customer service office to get it unblocked. It's silly.
If you enable Autoload on a Presto card which is below your chosen threshold, watch your balance. See whether Autoload actually succeeds or not. (The Presto website isn't always up-to-date. You may want to instead use a balance-checking machine or a self-serve reload machine to check your balance.) Then please click this link and tell us what happened.