Expounding on what Byzantine said,
Communications Instructions Radiotelephone Procedures, ACP 125 explains the difference thusly:
Roger: "I have received your last transmission satisfactorily." This does NOT imply intent to comply with the transmission.
Wilco: "I have received your last signal, understand it and
will comply." To be used only by the addressee (i.e. the
Commanding Officer). Since the meaning of
Roger is included in that of
Wilco, the two prowords are never used together.
To help you better imitate the way the real Navy signalmen do it, ACP 125 illustration acknowledgements by the following example, in this case between a surface action group flagship (ALFA ONE MIKE, or A1M) with the vanguard (FOXTROT SIX ROMEO, or F6R):
"When an originator desired confirmation that his message can (or will) be acted upon, he may request an acknowledgement from the addressee. The request is included in the text. The message is receipted for in the usual manner, but only the Commanding Officer or his duly authorized representative can acknowledge a message.
F6R-THIS IS A1M-SEARCH AREA BRAVO FOR POSSIBLE PLANE WRECKAGE-ACKNOWLEDGE-TIME 1445Z-OVER.
A1M-THIS IS F6R-ROGER-OUT.
If the commanding officer had heard and understood the message and directed acknowledgement, the operator would then have replied:
A1M-THIS IS F6R-WILCO (YOUR LAST TRANSMISSION)-OUT"