Mouse over a skill for a rough description of what it does. For more concrete numbers and percentages, you'll have to check around on the internet.
This depends on your choice of weapon, what monster you're hunting, and your personal preferences. It's also a topic of some contention among fans. When in doubt, try different skill combinations to see what works best for you.
Swapping different activated skills combinations without a lot of fuss is the point of an armor set searcher.
Check Kiranico to determine what monster drops are needed, which monster(s) those drops come from, and which quests are best to get those drops.
No sense duplicating all that information here.
Try selecting fewer activated skills, substituting skills that are cheaper in terms of decorations, or look for a better charm than the ones you have.
Don't forget to enter your best charms on the “Manage Charms” page so the searcher knows you have them.
By default, the set searcher will place pieces with any possibility of contributing into the armor piece lists (even if they contribute only a single skill point). The pieces which are the best candidates based on their skill points and slot counts will be selected by default.
You may wish to un-select armor pieces if they're too much of a hassle to forge, they don't have enough defense, or they just look hideous. Deliberately un-selected armor pieces will always remain un-selected on subsequent searches until you re-select them.
Conversely, you may wish to select extra armor pieces for the search if they have more defense (a blademaster helm instead of a gunner cap) or you've already forged them and want to see if they'll work. Just note that selecting many extra pieces may make the search take a lot longer.
The option to hide results with negative skills is available in an alternate stylesheet. In Firefox, you can find this under “View” → “Page Style” → “Hide Results With Bad Skills”
Chrome requires an extension to expose alternate stylesheet functionality, even though it's been part of the web specification since the dawn of time.
Your charms and other site defaults reside in your browser's local storage.
The CSV-formatted charms files are compatible with Athena's Armor Set Search. You can import files from those utilities into this armor search. You can export files from this armor search for those utilities. You can export files to use in another browser. You can even export files to have a local backup copy.
Mobile devices like smartphones and tablets don't handle file imports/exports very conveniently (if at all), and entering a lot of charms into a mobile device can be a hassle. Converting your charms list into a QR code allows you to easily transfer them to anything with a camera by using the appropriate buttons (“View Charms Code” on the device you're exporting charms from, and “Import Code Using Camera” on the device you're importing charms to).
Using the “Import Code Using Camera” button typically requires authorization, and the camera will remain active until it either finds a valid charms code or you cancel the search.