It's easy. You can switch out mirages in your party or switch the forms of mirages in your party at any save point or gate. Also, say you have 20 sp to spend with your chocochick, that amount is share between transfigurations. So you can spend 10sp on chocochick and 10 on chocobo, using up all your sp. If you unlock other mirage board (red chocochick in my example) and then switch to that form, all the sp you've earned for regular chocochick will exist for red chocochick. So even if you spend all 20 sp on chocochick and it's transfigurations, when you switch forms you'll immediately have that 20 sp to spend his you like on red chocochick.