this is just my opinion...
You could place an EQ first thing, even B-4 the sim, if you like. You could then also place an EQ AFTER the sim. Plus, there are EQ's in the sim (the tone knobs). Then, there are the tone knobs on the guitar which, in reality, are nothing more than high pass/low pass filters. So, in this example, you now have 4 stages of EQ. If you can keep it all straight, more power to you. If you need to simplify things, start cutting ur number of EQ's. Even with no EQ inserts, you'll still have at least a minimum of 2 stages of EQ: the guitar tone controls and the controls in the amp simulator. So you do the math and choose whichever makes you happiest.
As far as then NATURALLY miking the amp and ocmbining the two sounds, totally go for it. This can achieve a much more balanced and fuller sound. My advice in this instance is to record the amp in a totally dead space and THEN apply the space manually with a reverb on the track. This simply will give you much, MUCH more creative freedom during the session. (read on...)
Say, later in the session, you want to mix down and when you recorded the amp you recorded it in the middle of your living room and even turned on some reverb from the amp. This reverb, along with the acoustics of your room, is now printed to the track, along with your amp sound. Unless you 100% for sure, absolutely know this is what you want (my point being that being that sure is highly unlikely) then you now have a track that is printed eternally with a lot of ambience also.
I personally would also record the amp sound dry or as dry as I felt comfortable and, if I needed more space/natural ambience, add it with reverb or delays. This way, when you experiment during mixdown, you're options are completely open: recording with room ambience and/or amplifier reverb kind of cuts a lot of those options out when the track is printed while recording.
When you mix the two sounds together, if both are dry, once again, you will have many more options. Also, who's to say you don't end up dropping one sound or the other altogether. If you drop the DI in the mix and end up using only the miked amp, you will want a dry amp sound to play with. Again, these are simply opinions and there are no rules. Only artistic interpretation and variance from one engineer's technique to another. What one finds taboo may be the others crem de la creme.
