In order to see all of the tables in our companies DB I have to go find the main sys account. Is there a way to default my connection so that it shows the other users tables?
Going to Tools > Preferences > Database > Worksheet allows to set "default path to look for scripts".
In your SQL Developer screen shot you're looking at the 'Other Users' section of the navigation panel on the left, under your existing connection as SYS. and then if you run as a script the statements after that will be performed as that user - and it will disconnect and revert to SYS when the script finishes.
Any table that your connecting account has at least SELECT privileges on will show up in the "Other Users" node of the navigation tree. If the table does not show up there then it is a database permissions issue, not a SQL Developer configuration issue.
Think you don't want to repeated type otheruser.tablename in all your queries. If that is the case you want to run this
alter session set current_schema = otheruser;
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