Make sure you have an "apps" folder in the root of your SD Card
And when you do get apps make sure you rename the .dol file to boot.dol...
So for example.. if i were to download the
Homebrew Browser I would unzip the contents to my "apps" folder so it would be for example
F:\apps\Homebrew_Browser
or something relatively close.. to it.. then i would go inside.. and make sure that the dol file is named boot.dol (if not i would rename it to boot.dol)...
Optional: Check for "meta.xml" and "icon.png"... "those 2 make sure that it looks good in the homebrew channel and are not required"