If you use the standard version of our cart button codes and include at least one block of your View Cart code on every page, the cart should then appear as an overlay "inside" the page itself, so it fits within that site's existing branding; however, that would not allow adding items from different sites to a common cart order to check out together all at once.
If you use the non-javascript version of our Cart button codes, those will open the cart in a separate window/tab that can hold items added from separate sites to a common order together, but that cart could only display whatever custom logo/header you have uploaded to your E-junkie account. We have no way to alter the appearance of that cart nor the appearance of the checkout page for any type of cart implementation depending on which button on which site/page is clicked.
Buy Now buttons of course bypass the cart entirely and take buyers directly to instant checkout for just one item at a time, but they can't use any of our features that depend on the cart:
http://www.e-junkie.com/ej/help.buttons.buy-now.htm
You could at least make the cart and checkout page more generic by simply removing the custom logo/header image you'd uploaded to E-junkie. Just go to Seller Admin > Edit Profile, click Upload Your Logo, then use the Delete button on that screen to remove your custom header image. PayPal checkouts would then display whatever Business Name you have defined in your PayPal Profile, so you might want to change that to something suitably generic, and do likewise with the Display Name and Email settings in your E-junkie profile.
If you really want to maintain separate online business identities, you could really only do that with us by maintaining separate E-junkie accounts for each identity. Then you could specify a different Display Name/Email in each account's E-junkie Profile and upload a different custom logo/header image in each one. This would also allow you to set up each account with different account-wide settings under the Manage Your Seller Account section of their Seller Admin. If you still need to accept all payments to a common PayPal account for all sites, you would simply add secondary emails to your existing PayPal account and use those as the PayPal Email for each new E-junkie account.