The only issue you have is getting from Terminal 1 to Terminal 2; as its the only terminal that is not physically connected.
Your single entry visa should only be used on your return leg. You did not mention which airline you are using; but one can assume it is not Emirates since you are landing in Terminal 1.
The procedure for your wife will be the following (this only applies if her connection is less than 24 hours):
Once she arrives at Terminal 1, go towards Transfers and head for the Dnata transfers desk.
Show the Flydubai booking, and her baggage tags. If there is no interline agreement between her arriving airline and flydubai, she will have to pay a fee to transfer her luggage. If her baggage does not meet her flydubai ticket rules, she will also have to pay the extra / overage. I did a cursory check and Philippine Airlines does have an interline agreement with flydubai, so if she is flying on PR then her bags at Manila will be checked all the way through.
She will receive her flydubai boarding pass from the dnata transfer desk.
Dnata will arrange for a transit bus to Terminal 2
You can then meet her in the transit area of Terminal 2 (I suggest using Paul as a meeting place since it is a bit away from the normally crowded transit screening area and shopping area).
For all this, you do not need a transit visa - again, assuming the transit time is less than 24 hours.
On the return journey, both you and she will go through immigration - at that point her single entry visa will be utilized.