Firstly, if you go into the SRV while your ship is docked at a base landing pad... be sure to request permission from the base to dock while in the SRV. It's exactly the same as though you were going to land a ship at the base.
Then once you drive into the SRV garage under your ship, you can choose the "Board Ship" option. It's easy to find the right landing pad garage, just select your ship and it'll highlight exactly where it is. Drive into the SRV garage far enough, and "Board Ship" should be available.
IIRC, you can't "Board Ship" unless you request permission from the base first, though.
Your other option is simply to drive the SRV 2km to 3km away from the base, then choose "Recall Ship". It should leave the base on autopilot, and come land near you.
It's been a while since I've done these two things, but I'm pretty confident they still work.
Last edited by adlabs6; 05/12/18 11:45 PM.