Once you've set up your NmrResidues in your HSQC (or other base spectrum), you will need to peak pick your 3D spectra. You could do this by going to Spectrum / Pick Peaks / Pick ND Peaks... (or type PP). Here you can select an area in which you peak pick your 3D spectrum. The problem with this approach is that you can end up peak picking lots of noise peaks or artefacts and you won't be able to transfer your NmrAtom assignments from your HSQC to the 3D. A better way is to use the Pick and Assign module.
Open this module by going to Assign / Pick and Assign or typing PA. Go to the module settings by clicking on the gear icon. Select the spectrum display in which you would like to pick your 3D peaks (make sure that you have a spectrum display module with your 3D spectra open already - it can also be helpful to have another display open with your HSQC/base spectrum). You can make changes to the peak picking tolerances here if you decide this is necessary at a later stage. In the main Pick and Assign module, select your NmrChain from the drop-down menu. You will see that the table is now populated with all of your NmrResidues in this NmrChain. It is also useful to open the NmrAtom Assigner which you can do by going to Assign / NmrAtom Assigner or typing AN.
Begin the process of picking and assigning your 3D spectra by double-clicking on an NmrResidue in the Pick and Assign module table. Your spectra will automatically navigate to the position of this NmrResidue, so in your 3D spectrum display you should see a strip of peaks ready to be picked. Peak pick these by clicking on Restricted Pick in the Pick and Assign module. Remember that peaks are picked at the currently visible contour levels, so make sure that your levels are such that you won't pick lots of noise peaks. It can also be helpful to switch off the negative contour levels for spectra where you are not expecting any negative peaks (go right-click / Contours ... to do this). Now you can assign the H and N NmrAtoms from the HSQC to your newly picked peaks by clicking on Assign Selected. You can also do the peak picking and assignment in one go by clicking Restricted Pick and Assign. Finally, you just need to assign carbon NmrAtoms to the carbon dimensions of your 3D peaks. Select a peak (or several peaks which are all associated with the same carbon atom) and create a carbon NmrAtom by clicking on the CA, CB, CA [i-1], CB [i-1] or other assignment option in the NmrAtom Assigner. If you make a mistake, simply click on the same atom again to de-assign the peak(s) or directly click on the correct atom. You can see that your carbon assignments have been made in the Pick and Assign module table and that new NmrResidues and NmrAtoms have been created in the sidebar. When you have assigned the carbon dimension of all your peaks you are ready to move on to the next NmrResidue. Double-click on a new NmrResidue in your Pick and Assign table and repeat the pick and assign process.
Remember that some peaks in your HSQC (e.g. tryptophan side-chain peaks) may not have associated peaks in the 3D spectra.