Mac File Storage

I am transferring files to my new Mac and would appreciate some help to understand the Mac system with regard to file storage.
For example, I have my photos on a hard drive and they are filed in various folders for 2005, 2006 etc. Should I transfer these folders into iPhoto library or just leave them in the Pictures folder in Finder?

You can do it any way you please. You don't HAVE to use iPhoto, especially if there's another photo viewing app you prefer. iPhoto does offer the ability to categorize and sort your photos to a much greater degree, but it takes some time to really get a grasp on how it works.

Organization is up to you (as lifeisabeach said). One thing to note is that if you do use an app to organize your content (such as iPhoto or iTunes), it will organize your content for you. That bothers some people so I thought I'd just point that out to you in case.

In fact iPhoto organizes photos internally pretty much the same way you do (by year, then month, then day, then specific hours if there is more than one in a day).

The concept a lot of people can't seem to grasp is that it really doesn't matter how iPhoto organizes photos internally, it can show them to you pretty much any way you can imagine you might want them. The idea here is to the let the computer do the micro-management so you can focus on the things that are really important about photos: making them look their best, finding them and sharing them.