Coin collections can be meticulously organized,or resemble a hoard, as is the case with half of my collection, which are simply stored in various types of containers all mixed together. A true collection however is organized in such a way that one can preserve and admire the coins from time to time, as well as show them off to fellow collectors.
When coins are mixed together, the first priority is to separate your collection by type, series, and date. Why would it be important to separate 90% silver Walking Liberty half dollars, Franklin half dollars, and 1964 Kennedy half dollars? All are 90% silver and would have the same bullion value. The difference of course is that older coins would normally have a higher demand and greater numismatic value as a collectable coin. Mercury dimes are normally worth more than Roosevelt dimes for the same reason. In addition, once you separate the coins, it is much easier to search each series for those rare dates and die varieties.
If you have a large hoard of mixed coins, lay a large cloth on where you are going to separate them, and then gently dump the coins in the middle. Start separating the coins by type, starting with the largest denominations first as they are easiest to see and pick out. Obviously, if there are gold coins, remove them first. Silver coins are any three cent silver, half dime, dime, twenty cent pieces, quarter, half dollar, or dollar from 1964 or before, and nickels minted from 1942-1945 with the large mint mark above the dome of Monticello. It is important when searching through these piles, if you see brilliant uncirculated coins (you will know them when you see them), place them aside on a soft surface so as not to scratch or damage them.
Make a separate pile for each series starting with dollars, then halves, and so on. For coins in these series, as they are larger and heavier, they are more prone to denting if they are dropped on other coins. Stack them neatly or place them gently on a soft surface. At this stage you are not using a magnifying glass. Then continue with the quarters, and then dimes, keeping each series with each denomination separate. Most pocket-change collections have a pyramid-like number of coins for each denomination with the dollar at the top with the least number of coins, and the cents at the bottom with the most number of coins. As with most collections, the higher the denomination, the lower number of coins as part of the collection. Separating out the larger denominations first on these type of pocket-change collections also is more efficient as the nickel and cents are the most numerous part of the collection, and saving them for last makes it easier to separate.
After all coins are sorted by type, separate these by date and mint mark. The process is time consuming, but helps when evaluating and identifying any rare dates and die varieties. Once your collection is separated into their type/series, then you can move into the next step which involves searching for rare dates and die varieties. By focusing only on one type of coin at a time, it is much easier to utilize your numismatic resource of choice (ie. the Red Book).
I put my raw or ungraded coins into cardboard/mylar 2x2 holders and write any identifying information on the holder. This makes storage, organizing, and cataloguing much easier. There are several numismatic organizing software packages available on the market, but sites like numista.com and worldcoingallery.com offering cataloguing software that is just as good for free. I use numista.com because it can be imported to excel and tweaked to fit my wants and needs. Once your collection is organized and cataloged, it can be enjoyed much more, and makes insuring your collection, if you choose to do so, much easier.