1. No. Although I fail to see the logic of keeping the apk files for sideloading as opposed to installing from the store itself. The store may not be able to see your apk sideloads, and thus the apps may not update because you updated them via another method. Just go to the store and bookmark the webpages of the app you want.
2. As mentioned above no, but you can use several apps to back up the apk file like AppMonster. This is often done so that when you don't like a particular app update, you can revert back. However this is different from manual side load by getting apk's from obscure sources. The apk's wont be tampered with by anyone. Note that you cannot backup app data unless you are rooted. But installing an older version to overwrite the new one should not be deleting any data anyway.