How do we protect our IP efficiently as trade secrets?

Thinking that an "agreement with employees" is an efficient way to protect trade secrets is naïve. All that does is create a path to lawsuits with employees (or ex employees) and once the trade secret is revealed, it is gone!
A company must have a secure process of insuring that trade secrets are not easily available, are securely handled, and are only accessible to your most trusted employees. Depending on the trade secret, (formula, process, etc.), it may also be wise to create separate pieces that remain independent of any one person to have access to. If your business depends on the security of a trade secret, no measure is too extreme to protect it.

I agree and disagree with Edward.

A prudent IP protection plan deals with three components: inform, manage, mitigate. When you do all of these actions you will inculcate the importance of IP into your corporate culture.

While it is true that you shouldn't be naive and think that agreements will provide you protection, this doesn't mean that you shouldn't have clauses in your employment, vendor, and partner agreements so as to tell these people that you're serious about protecting your IP. I've recently written a LinkedIn article and blog post about this at http://wp.me/p4rYBE-20.

As part of your management strategy, you then decide which IP protection tool is best for you. If you don't have unique inventions that would allow you to receive patents then you can look at copyright or trade secrets. For software companies, the latter two are potentially stronger options than patents. If you choose trade secrets as your tool of choice then a best practice for trade secrets is to compartmentalize pieces of the secrets amongst those who need to have functional working knowledge so as to make your product or company better.

So now everyone in your company knows that you're serious about your IP, in order to mitigate any future challenges resulting from departures you need to have a plan. I suggest that when you fire an employee/vendor/partner or one of these leave your company, this person(s) should be required to sign a letter indicating that, despite their previous agreement, they will keep the information they've learned at the company confidential and will not use it for their own purposes for a reasonable period of time (say 2 years). Also, if this is an employee who quits or is fired, they should pack up their stuff and leave that day. There is no reason for this person to be hanging around writing more code, content or sales calls (or downloading your customer list).