How do I deploy an SSIS package? I am very new to SSIS. I have inherited a bunch of databases and SSIS packages.  I notice many jobs utilizing many different packages.  When I look at an existing job and try to see where a package it is using is located I just see that it is in the "SSIS Packages" folder. 

I know you can either deploy a package to the file system or as a database object(?).  How can I tell which type of deployment a package has taken?

Also, in an existing job, an associated SSIS solution where multiple projects contain multiple packages utilized by this job, there is one package I needed to modify. It isn't currently scheduled as part of a step of the job.  When I go to add the new step, I don't see as an option that I can choose this package. I assume it must not be deployed.  So how do I deploy it and how do I make sure I deploy it the same way the other packages in this job were deployed? (Really - how do I not mess things up!?)
How can I tell which type of deployment a package has taken?

Look at the definition of your SQL Agent Job Step. 

If it specifies /file then the package has been to deployed to the file system somewhere.

If it specifies /DTS then it's using a well known location on the SQL Server installation path (precise location eludes my memory as of this posting but \Program Files\Microsoft SQL Server\XXX\DTS\Packages and/or C:\Program Files (x86)\Microsoft SQL Server\XXX\DTS\Packages are good guesses)

If it specifies /sql then it is deployed to the specified SQL Server in msdb.dbo.sysdtspacakges90 (SQL Server 2005) or msdb.dbo.sysssispackages (SQL Server 2008/2008R2+)

As to scheduling a package that you can't see, this sounds suspiciously like you're not on 2008 R2 as you think but much more like 2012+ as this is the SSISDB with the folder/project/package structure. If this is the case, packages can be specified as being Entry Point Packages or not. It's just a UI convention, there's nothing that prevents them from running. There's a selector that specifies whether you want Entry Point Packages or All. Switch to All packages