Welcome to Tonequest 101. Lesson 1: Dialing-in a good clean tone.
Start with the tone controls set as 'flat' or 'neutral' as you can get them. The knob settings will be different for different amps. One reason I like my old Ampegs is the tone stack is an active boost/cut design which provides a wide range of adjustment. These controls have their minimum effect (no boost or cut) when the pointers are straight up (12 o'clock). Try setting your controls that way to start.
Roll your guitar tone controls down a bit; say 7 or 8 out of 10.
Start with your neck pickup. It will usually be warmer sounding than the bridge pickup, simply because the strings are less 'twangy' there. Work with one amp tone control at a time, raising or lowering the setting just a little bit, and trying that for a while. Don't make a lot of changes at once, because your ears will try to adapt to each change, and you end up getting lost. Just change one setting, just a little bit.
Then put your guitar down, and walk away for about 10 minutes. When you come back to your guitar, pay attention to your first impression of what it sounds like. Then change just one control a bit to try to correct anything that sounded 'wrong' when you first came back. Take another break to let your ears 'freshen up' again.
Again notice your first impression when you come back, and make another adjustment. You have to keep taking a break and coming back again, because your sense of hearing will always try to shift your 'normal' reference along with whatever change you make. You have to literally walk away, get into a different room, with different background ambience, in order to restore your auditory reference. Hey, if this stuff was simple and obvious, everyone
would have good tone, right?
You will not get the results you want in a few tries. Not even in the first day. The next day, you may decide that the settings that were wonderful for your last session now sound like ass. Keep at it, making small adjustments. There are reasons why you will see marks on the control panels of a lot of used amps.