i'm quite unsure what you meant by "base url/domain" but if you meant embed domain used in iframes / direct access to videos yes you have to replace it to the one given by panel unless you already use custom domain.
Sometimes files can be displayed delayed in the panel but they're there, we currently working on a solution to automatically update the files cache when file is uploaded via FTP. Regarding folders we're aware and this has been addressed in my earlier response on page number 4 in this thread.
Right now it's hard to tell that we will stick to mondays or switch back to daily payouts that are automatic. Please also note that currently we have some payout delayes due to ongoing transition into new platform.