Hi Krissi!
Congratulations on your upcoming visit to 
Walt Disney World! 
Thank you for bringing your question about your June vacation to 
planDisney! 
I was excited to see your question because I also visited Walt Disney World with my mom and we explored 
Magic Kingdom with her using an EVC. I was happy to discover that my mom was able to ride her ECV in most of the queues. This was great for her because she had difficulty standing for any period of time. There are a few queues that do not allow ECV access, such as 
Pirates of the Caribbean, 
Buzz Lightyear's Space ranger Spin, and 
Many Adventures of Winnie the Pooh. This isn't a complete list of the attractions in which ECVs are not allowed, just a few that I know about. 
However, don't worry about this at all because a Cast Member will tell you if an ECV is not allowed in the queue for a particular attraction. If that is the case, you may be directed to enter the attraction through the exit, asked to proceed down the FastPass line, or asked to transfer to a wheelchair. Regardless of which option is leveraged, you can be assured that mobility concerns are considered and solutions are available for every attraction.
I definitely would bring a cover, which can be as simple as a shower cap to cover the controls, or a rain poncho or plastic bag to cover the entire ECV. It rains frequently in Florida, so it's always a safe bet to be prepared.
While you are visiting Walt Disney World with your mom, I want to suggest a few mother-daughter activities. Consider booking a spa day at 
The Grand Floridian Spa. You both can enjoy a nice massage, manicure, pedicure, or facial and then relax in the relaxation room together. Another option is to make an 
advanced dining reservation at one of the many wonderful Disney restaurants. I personally love 
Flying Fish located at 
Disney's Boardwalk.I hope you have a magical vacation!
Magically
Stacy