Properly pricing jobs does take practice so if you feel like you cut yourself short on one job, try not to take it to heart and learn from it.
We never charged by the square footage because some homes are just weird shaped and some people would say for example, "Clean everywhere else, but the bedrooms." and that would be a headache to figure out what the square footage would be then. Unless you're a cleaning company that cleans the whole house or no house then the square footage thing isn't gonna work too well for you.
We charged a flat rate for the job they wanted. Sometimes we did custom cleans, they just tell us what they need, we mark it down, review the list with them, and are good to go. Other times, they wanted our basic clean for the whole house or a deep clean for the whole house. Sometimes they only want a deep clean in the bathrooms and basic the rest of the house so we'd adjust our price accordingly. We kind of had a feel over time what we would charge for a 2 bedroom or 3 bedroom or 5 bedroom or whatever it would be.
Also, a house cleaner in one town may not make as much as in the bigger city. Consider your town's median income. Our prices weren't able to be higher than so much because the median income here is lower. We found our groove after a while.
WP had a good post - definitely consider those factors mentioned fuel, supplies, etc. because that does cost you money.
We would charge a few dollars more for gas if our client were 15-30 minutes away as opposed to 5 minutes away.
You need enough to buy your supplies - get a feel of how much you're spending on supplies per house and what it costs to buy brand new bottles of your chosen cleaners. We did all natural cleaning supplies, but we had to factor in the cost to buy some of those cleaning solutions in bulk that we liked and the one we liked the most was not cheap at all. So, don't get caught off guard spending more than you need on supplies.
Definitely do a walk through. ALWAYS do a walk through of a home first. You may already do this since your mom has experience in the cleaning field. Never walk into a house sight unseen. When my husband and I first started, we got so excited when we got a huge move out clean. Little did we know, the guy downplayed the situation on the phone. It was a large 4 bedroom, 2 bathroom foreclosure that was totally trashed. A lot of personal belongings left behind. He already mentioned he took two loads to the dump in his truck. We spent 3-4 hours alone hauling trash out to the garage so he could take it to the dump. The real cleaning then started. It was so bad. It was definitely a smoker's home. One room was painted yellow, probably because of the staining, but when we scrubbed that wall, black was oozing out of it. No way to get it all cleaned with just sponge and water. Those walls needed replacing. That house was just grief and because we didn't see it first, we shorted ourselves money. Although, lesson learned! No house has been that bad since! Some people are uncomfortable with walk throughs or have never done them, but assure them they will get a free estimate and it's more fair to them because you're not over charging them (also fair to you so you know you're going to get your money's worth!). When both parties agree on a price and schedule a day, it's a great feeling.
Since it seems like you have a two person team, definitely count on the time. It takes my husband and I anywhere from 3-8 hours for a house, depending on the depth of the clean. Our longest job was like 14 hours (split into a few days) because it was a major move out/deep clean after someone had literally trashed the place.
Another lesson learned is employees. Are you planning to stay with just you two? My husband and I were a good duo team, but his health got worse and my health has gotten worse. I'm hurting all the time, I can't recover in a weekend and my husband's heart and lungs are bothering him more and more. Cleaning and exerting himself like he does isn't helping. Don't burn yourselves out. We couldn't find good, reliable help at all in our area and this hurt us more than anything else. We had so many clients we had no more availability and couldn't take any more, but our bodies can't handle all the work involved. We've pushed it too hard already.
If you do get help, be sure to find time to train them on how you all clean and finding someone reliable and with cleaning experience is great. Although, if you do hire employees, you may need to adjust your cost because you will need workman's comp if you hire employees (some people hire independent contractors because I think you can get away without the workman's comp, but that's not going to stop them from trying to sue you if they get injured on the job). If you need employees yet can't find the help, be prepared for that to because right now doesn't seem to be a good time for needing employees. Very hard to find (here where we are at least). Not to mention if you are insured as well, having employees will raise your insurance cost because your insurance/liability sometimes only covers 1-2 people so it will need to be changed if you have 3-4+ people. If you have employees then you'll also have to calculate on payroll. If you pay them out of pocket before payroll is set up, be prepared to pay back taxes. For employees, you would probably do a background check (usually anywhere from $50+ depending on how extensive the check is) or drug test - keep in mind those costs, too, in case you ever need to hire help. Keep in mind costs of any copies of paperwork that you may need from hiring employees, sometimes you may need to make copies of things. Also, set aside enough to pay taxes from your business in general.
Some other expenses that could catch you off guard are your internet bill (you may use it for marketing like Facebook ads or such), printer ink (if you print invoices for all or certain customers or you have to print them because you are a vendor for like an apartment complex so they can enter it into their system), paper clips/staples if you put your business card with a contract/service agreement/invoice, uniforms (we would use scrubs, some people have other preferences, but if you get them embroidered with names or simply a budget for replacing your uniform when they get holes or other wear), cases of damage - there might be times when something breaks or spills and it's a minimal cost (below $50 or so) so it's not worth the hassle of putting it through the liability insurance and easier to just go and buy and replace for the client at times.
*I'm sorry my post is long. Just figured I'd share what my husband and I learned while running our own business so that it can hopefully help you and your mother out