Hi,

Please edit counter up shortcode you want add  percent and add class to shortcode as screenshot http://prntscr.com/myc8p1

then go to Customize > Addtional CSS then add custom css to do that :

.add-precent-counterup .penci-cup-number-wrapper:before {
    content: '%';
    font-size: 35px;
    display: inline-block;
}

You can change font size is 35px to any font size you want 

Best Regards,

PenciDesign