Facebook pixel is a better solution for both building Custom Audiences (e.g. remarketing) and tracking any conversion (see image).
Custom Audience pixel will remain. However, it is advised to move to the new Pixel that enables to build everything.
The FB pixel can be implemented through Google Tag Manager or other tag management services, covering all pages of the website(s) along the customer journey.
There is no need to create and implement multiple Pixels as one can be shared among different Facebook Ad Accounts. Consequently, Custom Audiences and Custom Conversions can be created directly into each Ad Account according to specific needs.
* the Conversion tracking pixel will be disabled by the second half of 2016 as announced by #Facebook.