Uploading a custom logo is the only customization for PayPal Checkout that we support from our end; doing this would override any custom logo/header image URL specified in your PayPal account settings.
As for custom colors, you're welcome to set those up in PayPal and see if they show up in PayPal checkouts coming from your E-junkie buttons; however, I suspect those options mostly affected an older version of PayPal checkout and won't do much with the current PayPal checkout page. Indeed, I set up custom colors myself and found that apparently only the "Cart Area Gradient Color" had any effect.
