I record straight into Sonar. I have the "essentials" version so my EQ is limited in the channel strip. There is a basic EQ in there but I never use it.
You should be attempting to get a very clean and natural sound from your sources..... microphone, guitar processor, etc.... The goal is to get a natural sound into the track. Regardless of whether you have channel EQ or not, your aim should be to use as little EQ as possible on the tracks to get the job done. Some of the tracks, in some of the song projects I write and produce, have ZERO EQ on them. They are raw, just like they came into the DAW. That's because, in my humble opinion, listening to them on my studio speakers, they don't need any sonic shaping. Midi with good samples tends to fall into this category.
The engineer you described, setting at the board twirling knobs and moving faders is doing the job of evening out the sound as he/she hears it. Again.... the goal is to do as little to the sound at the board as needed to get that natural sound. The engineer is often having to deal with a variety of experience levels and gear quality on the other side of the glass. As home studio folks, we can often get things set up for consistent results without a bunch of board wizardry.
Recording raw, non-EQ'd tracks may not be your idea way to record. But if you don't have a board with EQ or an external EQ module, you have to record the tracks raw. So in those cases, popping some EQ into the track as an FX on playback is perfectly fine. It's exactly how I work. I have set up a number of my Cakewalk EQ's as presets to use for vocal, acoustic guitar, piano brighteners, drum and bass enhancers..... just so I don't have to start from scratch every time. Most EQ's use very little processing power on the modern computers so there's no problem with using them. I also use them on busses rather than always in the individual tracks.
So, all of my tracks go straight into Sonar directly from the mic with no pre processing to that point. That's not to say you can't do that, or shouldn't do that.... the important thing to know and understand is if you're going to use EQ pre or post..... know why you're using it and what it's doing to the sound.