no, you do not need to use the eCommerce Toolkit.
The checkout process that is created by the checkout wizard uses the information that the costumer enters on the checkout page when storing the order in the database, this is why you should not skip the checkout page. the eCart checkout process will not function properly if you bypass the checkout page, it may _seem_ extraneous, but is is necessary to the way eCart works.
If you do not want to use Express checkout, you can remove the express checkout button from the checkout page.
Yes, the api credentials are only needed for express checkout.
Please send a link to your site so I can test the checkout to see what is wrong.