The top area of the window displays the source and the target databases involved in merging.
In order to be able to merge between two databases, they need to
Whenever you merge into an existing database (DB) you need to 'Check IDs ...' before you will be able to transfer items (species, SAIs, trees, ...). This isn't necessary if you are exporting from a DB into a new DB (in which case the 'Check..'-buttons will be inactive)
After alignments and IDs have been synchronized, select any of the 'Transfer..'-buttons to transfer different items from the source to the target DB:
After you performed all wanted merges, you will like to save the target DB.
In case you were merging into the DB running in ARB_NT (see ´Merge data from another ARB database´) there is no need to save yet (therefore the buttons are inactive). Just close the ARB_MERGE window and save as usual in the ARB_NT main window.