Alana,
First, a look at your questions.
As for the htaccess file, that is the easiest. You need to do nothing. Ever (unless you want to add things like a 404 redirect which I admit I haven't gotten around to myself, but should; it would be nicer to have people find a nice looking page with a link to your home page instead of a sorry, not found).
What you have put in the htaccess can just stay there. It tells your site that you want it to look for includes when it loads files. Now you can put includes on any page you load, and if it finds the include as directed, it will load it into your file.
It is very easy to take down your old files. Really, unless you don't have some of the information (and you should have your backup files anyway) you can just go to the site through your ftp and delete anything you don't want there instead of downloading. For example, you want to leave the htaccess file. But you can just delete everything you don't want and then upload your new files.
As far as making an include of the sidebar, it is naturally up to you. If you are going to use one on several pages, make an include for it. You can name them sidebar1, sidebar2.....and so on and have several. Or if every page will be different just leave it on the pages and make no includes. It is all up to what you think will work best for you. You can put the code of some pages and put the include on others. Just because something is on one page doesn't mean you have to use it on others.
It is good that you are thinking about making these choices because there are lots of ways to do everything. You want to do it the way that is best for you.
If you do several sidebars, say three or four, and name one file sidebar1.html, for example, you would then use that name in the include statement, but you would not change the class name on the div tag in the code for it. That would stay the same. The width of the column, etc., is the same on all your pages so you want to be able to change all sidebars in that way and not need several css statements. (Forgive me if that sounds too obvious.)
What to do next? There are just a few things that relate to the process. First, your index page is complete. If you are having any problems with your work let me know.
For your template there are two ways to go. When you look at the index page there are only two sections left that are not includes (three if you do not do the sidebar). If you want you can make a separate template. Just take a copy of the index page and remove the information in the content section and sidebar, if applicable.
Be sure to leave the div tags, however, and everything else like all the includes.
You cannot remove much in the head, but you can remove the specific information that has been inserted. Just put things like [INSERT PAGE TITLE HERE].
Personally, I just use a copy of the index or other page, and make the necessary modifications. A lot of the head information can often stay the same and the page layout gives me suggestions and even some layout help. For example, I can just select the page header one (leaving the tags) and type in my new title. Then select and delete as I go along. Follow your own preference.
A little adjustment or two to make on the sidebar would help. As you go along you will find little things to fix and improve in your site that I did not focus in on. There are not many I hope, but some. For example, here is one that bears fixing and will only take a minute. Look at your side bar.
Look at the end of the first entry: ...Free Delivery"/></a> </p>. The is code for a space. Then notice the beginning of the next entry (<p> <a href="http://www.paidonresuand...">) and those after. There is another there. The net result is that the first item is not in line with the others in the column. All are centered, but the centering includes the extra spaces (a net of two on the combination).
All of these 's need to be deleted. Whenever space is needed on the sides or top of anything css "padding" should be used. For example, I think that it wouldn't hurt to put just a little space above the sidebar so it will not be so close to the google ad.
Old:
#sidebar {
padding: 10px;
float: right;
width: 160px;
text-align: center;
New padding line:
padding: 20px 10px 10px 10px;
Replace the padding statement in the first line with the new one. This puts 20 pixels on top instead of ten, then ten on the right, bottom and left. This small adjustment does make a nice improvement.
Good success with your site as you go forward. You will still have plenty of work bringing in the content from your old site, but it will be so much easier to work with in the future. You only need to work on the content div in each page. Everything else is done. For every page you have and for all you will ever make. What great news.
Let me know if I can help.