Once I have a list of phrases, rankings, and volumes from these tools, I'll look to internal tools (maybe Excel, Access, or another database) to organize, classify, and forecast opportunity. This is where I'll estimate a competitor's traffic based on volume & position CTR, set goals for a target position, and estimate traffic based off that position's CTR and keyword volume.
Long tail keywords can find people who are later in the buying cycle, and more ready to buy. For example, somebody searching for “tents” is probably early in the buying cycle, just starting to research what they want. Whereas somebody who searches for “North Face Kaiju 4 person tent” already knows what they want, and is more likely to be ready to buy.
What are people looking for on your site? These terms are keywords in the vocabulary of your actual audience and should definitely be added to your keyword list. Do not forget to look at the keywords people filled in that didn’t get any results: this was stuff people were expecting but didn’t find. You can look into the results of your internal search in Google Analytics at Behavior → Site Search → Search Terms.
I actually don't use any keyword tools aside from Google Trends, but only rarely do I even use that. I try to talk to many of our target audience members (entrepreneurs) as I can. I attend events, I have phone calls, I sit next to them while working. Generally speaking, I think it's a waste of time to START with keyword tools instead of actual customers. Yes, you can target people in broad swaths and get a high level sense for what's interesting and trending, but at least in the case of our business at NextView Ventures, it's way more powerful to talk to actual "customers" you serve.
The link back to googles API is crap – it keeps coming up with password authentication which renders it virtually useless when trying to find your own rank. Sells you the software initially. But then tries to sell you a load of stuff afterwards which effectively tells you the first version you have already paid for is useless without the extra “bonuses”. Not a nice way of doing business