You'll have to forgive me for my lack of familiarity of the Ptolus setting. I assume a lot of these questions can be answered in the fluff for that world, or explained by DM head canon. The following questions are what I would be asking myself about the space to help guide my design.

• What caused these tunnels to form? Erosion and dissolution, like irl caves, or something more fantastic, like the city formerly (or currently) being part of a Purple Worm's hunting grounds?
• Are there other creatures who live in the tunnels which could prove dangerous? Are they sapient or sentient? Do they hold a grudge against surface dwellers for any reason?
• Does the city attempt to manage these access points in any way? What form does that management take? Is there like a SWAT team of tunnel rats who get deployed whenever something reaches the surface, or are they proactively patrolling the tunnels to prevent incursions? Is there a records office which maintains a list sealed and unsealed entrances? How accurate is that list / how well-funded is that department?
• Does the Thieves Guild rely on greasing palms to keep their operation secret, or do they rely on the inherent danger / inaccessibility of the tunnels to operate?
• Is there a magic user within the Guild who could be responsible for setting up traps, surveillance, or alarms through magical means?
• Have members of the Guild put any effort into expanding / altering the tunnels they use most frequently? Are there capable diggers who would know how to do that well? If not, is there the possibility of a cave-in? Or, perhaps, did they contract out with the Stonecutter's Guild (for example) to ensure the work was done well? Is that an avenue for the players to get some extra information?

As far as general layout of the actual base, rather than the tunnels and subterranean access point, you mention it's in a mid-low income neighborhood, but you don't describe the building they occupy. Is it a house? A commerical venture of some kind? Does the guild attempt to keep up appearances by maintaining a cover of some kind? What sorts of apparatus would they need to keep that cover in place? If the building was originally a bakery, for example, do they continue to operate it as such? Are the employees of the front operation aware of the illicit activities they are covering up? Are they guild members, or are they civilians who are paid well enough not to ask questions?

I regret being all Socratic up in here, trying to answer your question with a series of questions, but I believe they will help you envision the requirements that a base like this would have, which will then guide what elements you need to include to achieve verisimilitude.