FireFox

When you say 'main Firefox' I take that to mean that you have a normally fully installed version of Firefox on your system (as well as having Firefox Portable on your system). For your main Firefox you should update that just as you normally did as if you did not have Firefox Portable on your system.

For your Firefox Portable you should never update it by downloading an update directly from Mozilla. Likewise you should never allow your Firefox Portable to automatically update itself. If you do any of those two things then the update file will come direct from Mozilla and using that can adversely affect the portability of your Firefox Portable.

How you do update Firefox Portable depends on whether you do or do not use the PortableApps.com Platform. If you do use the Platform (I don't) then I believe that you can let the Platform manage the update of your Portable Firefox. For detailed information on the Platform see the PortableApps.com Platform Support webpages.

If you do not use the Platform then you need to download the new Firefox Portable version yourself and install it manually (which is easy to do once you know how). If you do want to manually update yourself then only download the update file from this webpage: Firefox Portable Download -- to get language versions other than English US scroll down the page. Note that more often than not if a new version of Firefox has been released by Mozilla it can take quite some time before the new version of that is available as Firefox Portable released by PortableApps. Sometimes the new Firefox Portable version is released within a couple of days, sometimes it can take a couple of weeks -- so it's good to practice patience.

For general information on updating and managing PortableApps read all of the entries on this 'General' Support page. I strongly advise that you do this, it will take a little amount of time but you will learn a great deal about PortableApps in the process and the articles are not technically difficult to read.

For specific information on Firefox Portable read all of the information given on Mozilla Firefox, Portable Edition Support You need to be careful with some of the information given there as some of it is out of date, or about to become redundant because of changes Mozilla have/will be making to Firefox in the future.

In short answer to your questions: The reason why Firefox Portable always asks to update is that PortableApps.com make that setting to Firefox Portable to prevent the user from updating directly from Mozilla. The user can, of course, override that but you might severely compromise the portability of your Firefox Portable. And, yes, you do still need to update your 'main' Firefox installation just as you did normally in the past.