Firstly I would really look to introduce Ryder Matos into your cup team sharpish (Really settles well and is one of the best wonderkids I've found).
Gilardino would do well playing Advanced Forward or Poacher as long as Jovetic is in the team (Your main creative force), Montolivo is best used as a Deep Lying Playmaker Support or Advanced Playmaker Support. Jovetic at AML is better as an Advanced Playmaker Attack or if you want more width play him as a left Winger. If you want to play Jovetic up front with Gilardino then make Gilardino a Complete Forward Support and Jovetic as a Poacher. Or Jovetic as Deep Lying Forward Support and Gilardino Poacher. Vargas is a real commodity on the left Wing, play him as an attacking Winger or give him license at LB. In big games the Defensive Winger setting really helps keep the balance right (Vs Napoli/Inter I recommend that).
I would go 4-2-2-2 with Agyei and Montolivo sitting at DM (Montolivo Deep Lying Support and Agyei Anchorman) then Jovetic AML (Advanced Playmaker Attack) Cerci AMR (Winger Attack) and Gilardino/Silva Complete Forward Support/Attack (Depending on opponent) with Babacar as a Poacher.
Hope that shed some light on your dilemma...
First choice RB - Cassani, first choice LB - Vargas.
Really recommend you ease Ryder Matos in as soon as you can into that AMR slot, he's got immense potential. Explosive right winger who's a surprisingly good finisher with his head.