Alternate module folders

Modules technically can be in sites/default/modules. This just means though that the modules are only accessible to be used by the default site (which if there is only one site, is already the case). So while it's technically ok to be in that folder, it's true that the common recommendation is sites/all/modules, which makes the modules available to any multisites you are running on the same install. If you want to move them, the safest way is to disable all contributed modules (keep a log or screenshot to remember what to re-enable), then move the folders into sites/all/modules, then re-enable them. I've occasionally been able to move the modules without disabling them, but sometimes this causes errors, so the safest bet is to disable them first. Once you re-enable them, their location stored in the system table is automatically set to the new location. If something does end up stuck to the old path, you can manually edit the value in the database if you want, or run a quick query to replace the wrong paths.