I also started with Wheelock. After going through the main text (30+ years ago) I read through the texts in the Reader. Oh, and I studied privately with a great teacher (Dr. Richard Hebein at Bowling Green State University in Ohio USA).
A good methodology is what works for you. Many people here use Lingua Latina and/or D'Ooge to good effect, others use other texts.
"Good efect", however, is also a matter of your intentions. The variety of intentions re: learning Latin is well-displayed here on Textkit. Some want the mental exercise, some want to speak it, some want to read Augustan-age classics, some want to read the Bible and Patristic literature. A few of us even like reading the poetry. Some are more interested in the language per se.
The best advice I ever got was to 1) master the grammar essentials then 2) read, a lot. I'd now add 3) study Latin composition (if your intentions are serious enough).
When I began studying t'ai chi one of my teachers used to say "Ten years, good beginning". The truth is that *any* art requires a long apprenticeship, with typically from five to ten years of hard study. Since our schools don't seem to encourage this kind of involvement you'll have to find the strength for it within yourself.
We all want to improve our skills, and we must understand that regardless of method employed, it takes some serious amounts of time to master the language to the point of reading and comprehending at sight. Another anecdote from my t'ai chi studies: A student asked a teacher how long he'd have to work before he mastered the art. "Five years", replied the teacher. The student then asked, "What if I work twice as hard ?", to which the teacher responded "Ten years". The point is that mastery is far more than merely recognizing constructions. Vocabulary acquisition takes time, and then you need to read broadly enough to know the differences in usage. The assimilation of grammar, vocabulary, and usage simply takes time, and how much time it takes is very much a personal matter, even given optimal teaching methods.
But none of these hardships or difficulties should put you off from the task. "What is difficult is by definition not impossible". Know that the endeavor takes time and energy. Unless you're a Schliemann or Champollion or Lucus Eques you may need to make Herculean efforts in your passage to mastery. When you're flying through Liutprand or Petronius, you'll know why you made such efforts.
Btw: Yes, I can also write in Latin. But as Arnold Schoenberg wrote, "I'm not so interested in the fact that a man speaks Chinese. I'm interested in what he's saying." Composition is not a priority for me, but I will whole-heartedly agree with its recommendation towards quicker language mastery.
Similis sum folio de quo ludunt venti.