Usually when I've made them I just put sauce on top, not on the bottom, and just down the middle so the edges are exposed. And I make the sauce on the thick side so it is not too watery.
I bake them in the oven too, and they are never too soggy, but you could just grill to minimise the sauce absorption.
I've heard that corn tortillas are more resistant to going soggy than flour ones, but couldn't comment from experience.
If you want more flavour, add more flavour. That sounds like I'm being a smartass, but it's true. Starches absorb/obscure flavour, which is a large part of why both the nouvelle cuisine and the molecular (or whatever you want to call it; I hate that term) movements prize reductions and non-standard thickeners, respectively.
First of all, I'd echo Michael and suggest you not use a roux. That will instantly create more flavour (this is assuming you're keeping the roux blonde, and not cooking it darker for more intense flavour).
Second, you will want to introduce a liquid phase to the dip to keep it dippable as it cools while you eat it. I would suggest cream, or sour cream. Buttermilk would also be lovely for a nice tang. You won't need much, I would just substitute for the milk you are already using, and only use one cup to begin. Add more as needed to adjust consistency. Bring your liquid product to a slow simmer, and slowly whisk in your cheese until incorporated.
For the cumin, garlic, chiles, I would start by toasting the cumin in a hot dry pan, then add your olive oil, sautee the onions first (or even go so far as to caramelize, which would be lovely), then add and lightly cook the chiles and garlic. This will bring out more flavours.
I don't know what you mean by 'Queso' cheese; Queso is just Spanish for 'cheese.' Queso fresca? Queso blanco? But I would look for cheeses with more flavour. The ones you are using are fairly bland (comparatively) and will not provide an intensely cheesy experience.
Season at the end.
I would first, however, simply try making the same thing without a roux, and using half the milk. The flavour difference will be significant.
Best Answer
Depending on where you are, the word tortilla can mean a few different things. In Mexico it refers to a flatbread made of either wheat or corn and a few other ingredients. These flatbreads tend to come in standard sizes in the United States at least, one of which might be labeled the "burrito" size.
A burrito is one use for a tortilla. A burrito consists of a wheat flour tortilla wrapped around a filling. Often the filling might include beans, cooked meat, rice, and perhaps vegetables.