That is correct. They are interlinked. As it is shown in the picture, you can set different player values to increase, remain or decrease to your specification.
Under the 'Attributes' WILL NOT be frozen and under the 'Attributes to ignore' WILL be frozen. Making will be frozen on both side requires a source code change. Only the developers can do that. The way it is now is OK.
Although I have not frozen players for a while as it is not realistic, I am sure you can select multiple players and apply the freeze. When I did freezing, it was only for one player. The option to freeze when FMRTE starts is what you do to keep the players frozen. The game and your save HAS to be loaded in FM before you can open FMRTE to load your save to apply the freeze.
There is an FMRTE guide which is covers the various features and functions in FMRTE. You can find a link to it in my signature.