1. I don't want to use different Windows accounts.
2. Method Three here http://support.apple.com/kb/HT1495?viewlocale=en_US explains clearly how to create and use two different iTunes Libraries, in my case one Library for iPhone, the other one for iPod touch.
3. Backing up of (new) iPhone will create a file that is separate from the iPod's back up file and it's easy to recognize it in case there is a need to restore iPhone or iPod.
4. I can transfer all purchases from iPod or iPhone to iTunes, after iTunes is started with the appropriate Library for each device (by pressing Shift-Key before starting iTunes and selecting the Library). All the purchased apps will appear in their respective iTunes Library.
5. If I want to sync iPhone ONLY for apps (I don't want to sync iPhone Contacts, Calendars, Music....), I believe that syncing iPhone's apps will not erase anything from iPod touch or iPhone. Neither it will rearange the appearance of the apps on the iPod or iPhone Home screen. BUT I am NOT sure about this point.
6. If I want to add Music, Media, Podcasts, etc. - I can do it manually for both iPod touch and iPhone from their Library.