Custom email

One of my websites have full of custom plugins and functions. Upon invoice creation, invoice payment, product purchase, we send email using wp_mail().

I recently install this plugin which is working in user signup/password retrieval etc. but not in those custom email.

How can I use wp better email for all emails? Or how I should use wp_mail()?

PS: I’m using wp_mail() with content type HTML.

http://wordpress.org/extend/plugins/wp-better-emails/