OK, so here's what you need to do. You can select the base to land next to it doing a manual landing. How you do this will depend on the gravity of the moon/planet.
If it's below 0.5g, fly towards the planet and try to keep the angle of descent at around 25 - 30 degrees to make life easy. Eventually you'll hit glide altitude where you'll approach the surface. Once you've exited glide, throttle down immediately to stop. Then get your bearings, throttle up into the blue zone and approach the base.
Find a suitable place outside any exclusion zone (you'll know when you hit one), cut the throttle and gently descend to about 100m. Deploy landing gear and look for a blue dot on the surface under the HUD image of your ship where the radar was a moment ago. If it's not blue, increase throttle gently and look for a flatter area. Once you have a blue dot, cut throttle and very slowly descend until you've hit the ground and your engines shut down.
Then deploy your SRV and drive over to the base.
If gravity is above 0.5g just approach at a shallower angle (15- 20 degrees) and be a little more gentle with the controls.
Bit of practice and you'll be fine.