The token action bar at top is meant to be used for either Actions (character specific macros written on the character sheet that apply to the selected character/token), or macros written for universal access by all characters/tokens, based upon the token which is selected. An example of the former might be an attack or spell, an example of the latter might be an initiative macro meant to be used by anyone but that specifically acts upon a selected token. They are situational. They are not meant for general all-the-time-use.
The macro bar at the bottom is meant to hold macros that do not require a token to be selected to activate. They are macros that might call up a handout lore document, or call up a chat menu, or display information in the chat log.
These are generalizations, because there is considerable freedom in macro writing. It looks like you have written a lot of general macros and told them to be token macros, meaning they will only appear when a token is selected. If your intent was for them to be available to all players, fill in "All Players" in the macro editing box. It will be up to them whether they want them to appear in the macro bar. That setting is handled by clicking "show in bar" on the collections tab. Essentially, by assigning them to all players, you are causing them to be available in the collections tab.
If you do not want any macros to appear in the token action bar, do not assign them to be token actions.
It looks like you have written your macros in a way not intended for them to be used. People are trying to help you here, but please realize if you did not use them correctly in the first place, they will require work to correct. There is nothing wrong with the system, you have simply not used it as intended, and now are getting undesirable results. If you would like some help or guidance on how to correct your macros, please post the text of a few and we can hopefully work out a solution that won't require too much hassle.