Just some quick thoughts (I'm typing this from my phone).
I'd recommend checking out Santa Fe and/or Albuquerque for places to stay. What type of lodging are you looking for? What price range? Do you want to stay in the same place both nights or does that not matter?
Some preliminary places/sights to consider: Pecos National Historical Park (on your way to Santa Fe), Bandelier National Monument (half day trip from Santa Fe), Kasha-Katuwe Tent Rocks National Monument. Taos Pueblo is a near must see when in northern NM but not sure if that would work with your plans. Perhaps rather than taking I-25 to Santa Fe, there's a longer route via Taos (others will have to confirm this). Alternatively, Taos/Taos Pueblo can be a full day trip from Santa Fe. Head to Taos via the Low Road and back to Santa Fe via the High Road for the best views in your windshield.
Many, many, many more options. If you tell us more what you enjoy doing (scenic driving, hiking, shopping, art, museums, spas, relaxing, culture, history, food, etc.), we can give far better advice.
Finally, when are you travelling? Can make a difference as far as advice.
Of course, your interests would help. Perhaps you'd like a 2nd night in Gallup at the old historic route 66 hotel El Rancho. You might find it interesting:
Thanks for the advice, I will be travelling in early April.
I will be travelling with my wife & 15 year old son, we are intested in Scenic drives and local historic sites.
Would prefer to break the journey with two seperate overnights.
It's not for everybody but in Holbrook Az is a Wigwam motel, one of the three left in the USA. Vintage cars outside. It's basic and close to the trains. Before Holbrook you'll find Petrified Forest NP.
Another classic place is in Winslow at La Posada. This place has an excellent restaurant but maybe it's too close to Flagstaff already. Lots of places for R66 between ABQ and Flagstaff. A scenic drive in NM is via NM53 to El Malpais NM, El Morro NM and Zuni Pueblo.
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