Investing when you have less than 20% equity in current home

[Ariel Herrera]

I recently purchased my first home with 5% down. I am house hacking by having a roommate pay a portion of the rent. 

After the mortgage, utilities, and other expenses I estimated that I can save about 30% of my salary earnings after taxes. My goal is to buy another property in 2-3 years to either live in (then rent 1st property) or rent out (then stay in 1st property). 

I am concerned if I save enough to put 20% down on a property 2 years from now but still have low equity in my current home how that will affect my ability to get a loan.

Should I use the savings to apply extra payments to the mortgage to have more equity (20%) ? Or would it be more beneficial to pay the mortgage as is and save solely for the future investment property?