Nope, no 100% way to guard against skin-transmitted STDs.
However, there are ways to reduce your odds of catching them. Check out this article, in which I discuss them:
How to Avoid STDs Even If You Have Lots of Sex
That said, like you saw, you won't always be able to tell from examining her. Sometimes there's no obvious sign.
As for what to do if you have them, bit of a tough call, that.
I guess if you're the most responsible man on the planet, you can just go full abstinence until the infection completely clears.
If you're of the more human variety, however, my recommendations would be to always wear a condom until you're completely in the clear, and if there are physical signs (warts, scales) you may want to laser those rather than wait for them to clear on their own... which can take a while (up to a year).
If you have the permanent/incurable type, like genital herpes, then it's especially tough, because you're always contagious. Obviously don't shag when you have an outbreak, and if you do shag, always wrap it up so you reduce your odds of passing along... but you can't get those odds to zero. So think very carefully about what women you're shagging (probably shouldn't shag any virgins you could pass it to).
I wouldn't worry too much about it until you end up in the situation again.
When you do, you'll have to do some soul searching and decide what the right path to take is.
I know some guys with these who convince themselves they're not contagious. But you are. So, that in mind, decide what you'll do.