It sounds like your friend Zetr0 took care of you very well with the HD and it's jumper settings.
The SCSI interface is versatile, but, has a small learning curve. If you ever hope to get more from this system (CD reader or writer, Zip drive, one of Mechy's card readers, etc), you should read up on SCSI termination, IDs, etc. I'll bet Wikipedia has some good stuff.

For now, I think you're good to go.
None of the Amiga ports are "hot pluggable" (The power must be OFF to add or remove a cable!). Most ports will survive a couple of accidents, but, the damage is accumulative. One day the port will simply stop working. Fortunately for you, the A500 has socketed chips and can be repaired easily.
The parallel port is particularly useful. You can get sound samplers (like GVP's DSS8+), hardware MP3 decoders (like MasPlayer), video enhancement (DCTV, GVP's G-Lock), etc. Many of these take some patience to find today.