The important thing to remember is there is no "supposed to" or "best way". There's what works for you and you photos. This may be iPhoto or some other app.
Couple of thoughts: iPhoto is not an editor. It's a Manager - like Contacts for your Addresses or iTunes for your Music, it offers powerful and easy to use tools that will help you manage and share your photos in the various ways you might need it. It will also enhance and crop and edit photos as well, but if you're not using it as a manager then forget about it for editing as it will be just too complex. There are loads of editors out there.
If you use iPhoto then it's your "go-to" for anything to do with your Photos. Viewing, Organising, sharing, Uploading, Printing, whatever. All of these things can be done either with or via iPhoto. Put another way, you never access your files via the Finder.
For more on this see this User tip:
https://discussions.apple.com/docs/DOC-4491
There are two ways to set up your iPhoto Library. Managed and Referenced
A Managed Library, is the default setting, and iPhoto copies files into the iPhoto Library when Importing. The files are then stored in the Library package
A Referenced Library is when iPhoto is NOT copying the files into the iPhoto Library when importing because you made a change at iPhoto -> Preferences -> Advanced. (You unchecked the option to copy files into the Library on import) The files are then stored where ever you put them and not in the Library package. In this scenario you are responsible for the File Management.
As you are new to iPhoto I strongly urge you to run a Managed Library. There are many pitfalls with a Referenced one - see here for instance
https://discussions.apple.com/thread/3062728?tstart=0
and for someone new to iPhoto and The Mac you can lose data very easily with a Referenced Library.
However you store the files, importing is the same: easiest way: drag a folder of images to the iPhoto Window and iPhoto will import it and create an Event from it.
If you have a managed library then it will copy the files into its own Library. You filing structure is then pointless. You can trash it - but don't do it immediately. iPhoto is a great app, but it's not necessarily for everyone. When you've lived with it for a few weeks and are sure it's for you, that's when you can trash your own filing structure.
The problem with what you have now - files-in-folders-and-subfolders - is that it is limited. Searching is trcky as you don't have a whole lot of things to search on. I append the following to show you some of the options available in iPhoto.
I use Events simply as big buckets of Photos: Spring 08, July - Nov 06 are typical Events in my Library. I use keywords and Smart Albums extensively. I title the pics broadly.
I keyword on a
Who
What
Where basis (The When is in the photos's Exif metadata). I also rate the pics on a 1 - 5 star basis.
Using this system I can find pretty much find any pic in my 44k library in a couple of seconds.
So, for example, I have a batch of pics titled 'Seattle 08' and a typical keywording might include: John, Anne, Landscape, mountain, trees, snow. With a rating included it's so very easy to find the best pics we took at Mount Rainier.
File -> New Smart Album
set it to 'All"
title contains Seattle
keyword is mountain
keyword is snow
rating is 5 stars
Or, want a chronological album of John from birth to today?
New Smart Album
Keyword is John
Set the View options to Sort By Date Ascending
Want only the best pics?
add Rating is greater than 4 stars
The best thing about this system is that it's dynamic. If I add 50 more pics of John to the Library tomorrow, as I keyword and rate them they are added to the Smart Album.
In the end, organisation is about finding the pics. The point is to make locating that pic or batch of pics findable fast. This system works for me.