I have been using a site submission tool for sometime now and wonder if it is better to submit manually.

Dare I say the name of the product that I am using? What is the etiquette about naming names?

I would think that it is fine to name names......the forum is full of named programs....

Anyone think that using WebPosition as the submit tool is wise or is the manual submition process preferred by the Search Engines?

Most search engines guidlines state that they prefer manual.

I've always done manual submissions, actually, I haven’t done a submission for some time now with new sites, basically I just go out and get the site listed in legitimate directories and let the engines come and crawl their way to it.

have a great weeknd!

As I go through the manual process, I notice that many SE's are charging for adding the URL. I wonder if this is what will be the norm as the years go by.

Some SE's used to charge but dropped it due to lack off responce. Most of the big search engines like Google you don't need to submit too as Marc points out, just get a link from a site within Google's index and your site will be crawled and indexed.

To check to see if a site is indexed (or more importantly the page your link will be on) you can click on the cached snap shot of page from the Google bar (if you have it installed) or do a search in Google as follows.

cache:URL of site

If it brings up no result, its not in the index.

For Google, you do not have to submit directly. Just get a PR5 link from a good source. your site will get spidered shortly.

For Yahoo , there is a free submission.

MSN, There is no free submission at present. But you can get into via backdoor ( such as directory listings)

It might be useful to get into other search engines too. such as Gigabot, TyGo etc.,

For directory listings, try it manually.
DMOZ, Yahoo etc.. needs manual submission.