If your wife has her passport then consider a short trip with her to Hong Kong or somewhere in SEA then when you travel back to Philippines just request a Balikbayan visa which will entitle you to stay for up to one year. Your wife must be with you on entry and it may help if you have a copy of your marriage certificate with you.
Or arrange your outward flight via Bangkok,KL or HK and have your wife meet you there then travel to Philippines together
Extending your visa is relatively easy,its P3030 for 59 day extension and I believe you will be required to secure an alien certificate of registration (ACR) after the second extension